Index

A

Ab1 (class in galaxy.datatypes.binary) access_action() (galaxy.webapps.galaxy.controllers.external_services.ExternalServiceController method) accumulate_tool_dependencies() (in module tool_shed.util.common_util) act_on_multiple_datasets() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) Action (class in galaxy.security) (class in galaxy.webapps.tool_shed.security) ACTION_NAME (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper attribute) action_name (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper attribute) ACTION_NAME (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper attribute) action_name (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper attribute) action_type (in module galaxy.tools.parameters.output) ActionBox (class in galaxy.jobs.actions.post) ActionInputError actions (galaxy.jobs.actions.post.ActionBox attribute) ActionSection (class in galaxy.external_services.service) activatable_datasets (galaxy.model.History attribute) activatable_folders() (in module galaxy.webapps.galaxy.controllers.library_common) activatable_folders_and_library_datasets() (in module galaxy.webapps.galaxy.controllers.library_common) activatable_library_datasets (galaxy.model.LibraryFolder attribute) activate() (galaxy.webapps.galaxy.controllers.user.User method) (pkg_resources.Distribution method) activate_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) active (galaxy.model.WorkflowInvocation attribute) active_contents (galaxy.model.History attribute) active_datasets_children_and_roles (galaxy.model.History attribute) active_folders() (in module galaxy.tools.actions.upload_common) (in module galaxy.webapps.galaxy.controllers.library_common) active_folders_and_library_datasets() (in module galaxy.webapps.galaxy.controllers.library_common) active_repositories (galaxy.webapps.tool_shed.model.User attribute) add() (galaxy.managers.citations.CitationCollection method) (galaxy.util.streamball.StreamBall method) (pkg_resources.Environment method) (pkg_resources.WorkingSet method) add_api_controller() (galaxy.web.framework.base.WebApplication method) add_composite_file() (galaxy.datatypes.data.Data method) add_data_table_watch() (galaxy.datatypes.display_applications.application.DisplayApplication method) add_dataset() (galaxy.model.History method) add_dataset_collection() (galaxy.model.History method) add_deserializers() (galaxy.managers.base.ModelDeserializer method) (galaxy.managers.hdas.HDADeserializer method) (galaxy.managers.histories.HistoryDeserializer method) add_display_app() (galaxy.datatypes.data.Data method) add_display_application() (galaxy.datatypes.data.Data method) add_dummy_datasets() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) add_entries() (galaxy.tools.data.ToolDataTable method) add_entry() (galaxy.tools.data.ToolDataTable method) (galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager method) (pkg_resources.WorkingSet method) add_external_service_association() (galaxy.model.RequestType method) add_folder() (galaxy.model.LibraryFolder method) add_galaxy_session() (galaxy.model.History method) add_history() (galaxy.model.GalaxySession method) add_history_datasets_to_library() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) add_implicit_input_collection() (galaxy.model.HistoryDatasetCollectionAssociation method) add_implicit_output_dataset_collection() (galaxy.model.Job method) add_input() (galaxy.model.WorkflowInvocation method) add_input_dataset() (galaxy.model.Job method) add_input_dataset_collection() (galaxy.model.Job method) add_input_library_dataset() (galaxy.model.Job method) add_item() (galaxy.external_services.service.ExternalServiceActionsGroup method) add_item_annotation() (galaxy.model.item_attrs.UsesAnnotations method) add_library_dataset() (galaxy.model.LibraryFolder method) add_metric() (galaxy.model.HasJobMetrics method) add_new_entries_from_config_file() (galaxy.tools.data.ToolDataTableManager method) add_option() (galaxy.web.form_builder.SelectField method) add_output_dataset() (galaxy.model.Job method) add_output_dataset_collection() (galaxy.model.Job method) add_output_library_dataset() (galaxy.model.Job method) add_parameter() (galaxy.model.Job method) add_post_job_action() (galaxy.model.Job method) add_repository_registry_entry() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method) add_route() (galaxy.web.framework.base.WebApplication method) add_sample() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) add_samples() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) add_serializers() (galaxy.managers.base.ModelSerializer method) (galaxy.managers.hdas.HDASerializer method) (galaxy.managers.histories.HistorySerializer method) add_species() (galaxy.tools.util.maf_utilities.RegionAlignment method) add_sreg() (galaxy.web.framework.openid_manager.OpenIDManager method) add_tag_async() (galaxy.webapps.galaxy.controllers.tag.TagsController method) add_template() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) add_ui_controller() (galaxy.web.framework.base.WebApplication method) add_ui_controllers() (in module galaxy.webapps.reports.buildapp) (in module galaxy.webapps.tool_shed.buildapp) add_validation_error() (galaxy.model.DatasetInstance method) add_view() (galaxy.managers.base.ModelSerializer method) add_visualization_revision() (galaxy.web.base.controller.UsesVisualizationMixin method) addAttributesToRoot() (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method) addChildNode() (galaxy.visualization.data_providers.phyloviz.baseparser.Node method) addChildrenToJson() (galaxy.visualization.data_providers.phyloviz.baseparser.Node method) AddFrameData (class in galaxy.webapps.galaxy.controllers.tool_runner) adding_to_library_dataset_files (galaxy.model.Sample attribute) AdditionalValueFilter (class in galaxy.tools.parameters.dynamic_options) addMiscToJson() (galaxy.visualization.data_providers.phyloviz.baseparser.Node method) AddressField (class in galaxy.web.form_builder) addRoot() (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method)

Admin (class in galaxy.web.base.controllers.admin) admin_role (galaxy.webapps.tool_shed.model.Repository attribute) AdminActions (class in galaxy.actions.admin) AdminController (class in galaxy.webapps.tool_shed.controllers.admin) AdminGalaxy (class in galaxy.webapps.galaxy.controllers.admin) AdminRepositoryGrid (class in tool_shed.grids.admin_grids) AdminRepositoryGrid.DeletedColumn (class in tool_shed.grids.admin_grids) AdminRequestsGrid (class in galaxy.webapps.galaxy.controllers.requests_admin) AdminRequestsGrid.UserColumn (class in galaxy.webapps.galaxy.controllers.requests_admin) AdminRequiredException AdminToolshed (class in galaxy.webapps.galaxy.controllers.admin_toolshed) Affybatch (class in galaxy.datatypes.genetics) after_setting_metadata() (galaxy.datatypes.data.Data method) AliasPickleModule (class in galaxy.util.aliaspickler) AliasUnpickler (class in galaxy.util.aliaspickler) Alignment (class in galaxy.datatypes.sequence) all_eggs (galaxy.eggs.Crate attribute) all_missing (galaxy.eggs.Crate attribute) all_names (galaxy.eggs.Crate attribute) all_roles() (galaxy.model.User method) (galaxy.webapps.tool_shed.model.User method) allow_action() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.HostAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) allow_action_on_libitems() (galaxy.security.GalaxyRBACAgent method) allow_datatype_change (galaxy.datatypes.assembly.Velvet attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.genetics.RexpBase attribute) (galaxy.datatypes.genetics.Rgenetics attribute) (galaxy.datatypes.interval.BedStrict attribute) (galaxy.datatypes.ngsindex.BowtieIndex attribute) allow_push() (galaxy.webapps.tool_shed.model.Repository method) allow_user_access() (galaxy.tools.DataManagerTool method) (galaxy.tools.Tool method) allowed() (galaxy.web.framework.helpers.grids.GridOperation method) always_conditional (galaxy.eggs.GalaxyConfig attribute) Amos (class in galaxy.datatypes.assembly) amount (galaxy.model.Quota attribute) annotate_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) annotation_assoc (galaxy.managers.hdas.HDAManager attribute) (galaxy.managers.histories.HistoryManager attribute) annotation_mapping() (in module galaxy.model.mapping) anon_user_api_value() (galaxy.webapps.galaxy.api.users.UserAPIController method) anonymous (galaxy.managers.context.ProvidesUserContext attribute) api_key() (galaxy.webapps.galaxy.api.users.UserAPIController method) api_keys (galaxy.webapps.tool_shed.model.User attribute) api_keys() (galaxy.webapps.galaxy.controllers.user.User method) api_path (galaxy.jobs.deferred.pacific_biosciences_smrt_portal.SMRTPortalPlugin attribute) api_payload_to_create_params() (in module galaxy.managers.collections_util) ApiKeyManager (class in galaxy.managers.api_keys) APIKeys (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) app_factory() (in module galaxy.webapps.reports.buildapp) (in module galaxy.webapps.tool_shed.buildapp) append() (galaxy.datatypes.metadata.MetadataSpecCollection method) (galaxy.model.custom_types.MutationList method) append_quality() (galaxy_utils.sequence.sequence.SequencingRead method) append_sequence() (galaxy_utils.sequence.sequence.SequencingRead method) apply_action() (galaxy.tools.parameters.output.FormatToolOutputAction method) (galaxy.tools.parameters.output.MetadataToolOutputAction method) (galaxy.tools.parameters.output.ToolOutputAction method) (galaxy.tools.parameters.output.ToolOutputActionConditional method) (galaxy.tools.parameters.output.ToolOutputActionConditionalWhen method) (galaxy.tools.parameters.output.ToolOutputActionGroup method) apply_galaxy_conventions() (galaxy_utils.sequence.fastq.fastqCSSangerRead method) (galaxy_utils.sequence.fastq.fastqSequencingRead method) apply_item_tag() (galaxy.managers.tags.TagManager method) apply_item_tags() (galaxy.managers.tags.TagManager method) apply_query_filter() (galaxy.web.framework.helpers.grids.Grid method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid method) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid method) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid method) (galaxy.webapps.galaxy.controllers.library.LibraryListGrid method) (galaxy.webapps.galaxy.controllers.page.HistoryDatasetAssociationSelectionGrid method) (galaxy.webapps.galaxy.controllers.page.HistorySelectionGrid method) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid method) (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid method) (galaxy.webapps.galaxy.controllers.page.PageListGrid method) (galaxy.webapps.galaxy.controllers.requests.UserRequestsGrid method) (galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid method) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid method) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid method) (tool_shed.grids.admin_grids.RoleGrid method) approve_repository_review() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) approved (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) approved_states (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) archive_dir (galaxy.eggs.scramble.ScrambleEgg attribute) archive_download() (galaxy.webapps.galaxy.api.histories.HistoriesController method) archive_export() (galaxy.webapps.galaxy.api.histories.HistoriesController method) as_dict() (galaxy.webapps.tool_shed.model.SkipToolTest method) as_display_type() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) as_gbrowse_display_file() (galaxy.datatypes.tabular.Tabular method) as_requirement() (pkg_resources.Distribution method) as_ucsc_display_file() (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.interval.Bed method) (galaxy.datatypes.interval.BedGraph method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.Tabular method) asbool() (in module galaxy.util) ascii_max (galaxy_utils.sequence.fastq.fastqCSSangerRead attribute) (galaxy_utils.sequence.fastq.fastqIlluminaRead attribute) (galaxy_utils.sequence.fastq.fastqSangerRead attribute) (galaxy_utils.sequence.fastq.fastqSequencingRead attribute) (galaxy_utils.sequence.fastq.fastqSolexaRead attribute) ascii_min (galaxy_utils.sequence.fastq.fastqCSSangerRead attribute) (galaxy_utils.sequence.fastq.fastqIlluminaRead attribute) (galaxy_utils.sequence.fastq.fastqSangerRead attribute) (galaxy_utils.sequence.fastq.fastqSequencingRead attribute) (galaxy_utils.sequence.fastq.fastqSolexaRead attribute) assert_sequence_quality_lengths() (galaxy_utils.sequence.fastq.fastqCSSangerRead method) (galaxy_utils.sequence.fastq.fastqSequencingRead method) associate() (galaxy.managers.base.ModelManager method) associate_action_dataset_role() (galaxy.security.GalaxyRBACAgent method) associate_components() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) (galaxy.webapps.tool_shed.security.RBACAgent method) associate_group_role() (galaxy.security.GalaxyRBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) associate_repository_category() (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) associate_user_group() (galaxy.security.GalaxyRBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) associate_user_role() (galaxy.security.GalaxyRBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) (galaxy.webapps.tool_shed.security.RBACAgent method) ASync (class in galaxy.webapps.galaxy.controllers.async) async_template (galaxy.web.framework.helpers.grids.Grid attribute) AsyncDataSourceTool (class in galaxy.tools) AsynchronousJobRunner (class in galaxy.jobs.runners) AsynchronousJobState (class in galaxy.jobs.runners) AttributeValueSplitterFilter (class in galaxy.tools.parameters.dynamic_options) AuthenticationController (class in galaxy.webapps.galaxy.api.authenticate) AuthenticationFailed AuthenticationRequired AvailableDistributions (in module pkg_resources) Axt (class in galaxy.datatypes.sequence)

B

BadValue (class in galaxy.tools) Bam (class in galaxy.datatypes.binary) Base (class in galaxy.util.inflection) base (galaxy.web.framework.base.Request attribute) (galaxy_utils.sequence.transform.ColorSpaceConverter attribute) base_dataprovider() (galaxy.datatypes.data.Data method) Base_Parser (class in galaxy.visualization.data_providers.phyloviz.baseparser) base_to_color_dict (galaxy_utils.sequence.transform.ColorSpaceConverter attribute) BaseAnnotationsController (class in galaxy.webapps.galaxy.api.annotations) BaseAPIController (class in galaxy.web.base.controller) BaseCitation (class in galaxy.managers.citations) BaseController (class in galaxy.web.base.controller) BaseDataProvider (class in galaxy.visualization.data_providers.basic) BaseDataToolParameter (class in galaxy.tools.parameters.basic) BaseExtendedMetadataController (class in galaxy.webapps.galaxy.api.extended_metadata) BaseField (class in galaxy.web.form_builder) BaseItemTagsController (class in galaxy.webapps.galaxy.api.item_tags) BaseJobMetric (class in galaxy.model) BaseJobRunner (class in galaxy.jobs.runners) BaseParamParser (class in galaxy.web.params) BaseProvenanceController (class in galaxy.webapps.galaxy.api.provenance) basestring() (galaxy.managers.base.ModelValidator method) basestring_list() (galaxy.managers.base.ModelValidator method) BaseUIController (class in galaxy.web.base.controller) BaseURLToolParameter (class in galaxy.tools.parameters.basic) Bcf (class in galaxy.datatypes.binary) Bed (class in galaxy.datatypes.interval) Bed12 (class in galaxy.datatypes.interval) Bed6 (class in galaxy.datatypes.interval) BedGraph (class in galaxy.datatypes.interval) BedStrict (class in galaxy.datatypes.interval) before_setting_metadata() (galaxy.datatypes.data.Data method) begin() (galaxy.model.orm.logging_connection_proxy.LoggingProxy method) best_match() (in module mimeparse) (pkg_resources.Environment method) BIBTEX_UNSET (galaxy.managers.citations.DoiCitation attribute) BibtexCitation (class in galaxy.managers.citations) BigBed (class in galaxy.datatypes.binary) BigWig (class in galaxy.datatypes.binary) Binary (class in galaxy.datatypes.binary) biomart() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) Bmp (class in galaxy.datatypes.images) bool() (galaxy.managers.base.ModelValidator method) BooleanColumn (class in galaxy.web.framework.helpers.grids) BooleanExternalServiceActionsGroupWhen (class in galaxy.external_services.service) BooleanFilter (class in galaxy.tools.parameters.output) BooleanToolParameter (class in galaxy.tools.parameters.basic) BowtieBaseIndex (class in galaxy.datatypes.ngsindex) BowtieColorIndex (class in galaxy.datatypes.ngsindex) BowtieIndex (class in galaxy.datatypes.ngsindex) branch_deleted() (in module galaxy.webapps.galaxy.controllers.library_common) browse_categories() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_components() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) browse_datatypes() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_deprecated_repositories_i_own() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_external_services() (galaxy.webapps.galaxy.controllers.external_service.ExternalService method) browse_form_definitions() (galaxy.webapps.galaxy.controllers.forms.Forms method) browse_libraries() (galaxy.webapps.galaxy.controllers.library.Library method) (galaxy.webapps.galaxy.controllers.library_admin.LibraryAdmin method) browse_library() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) browse_my_writable_repositories() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_my_writable_repositories_missing_tool_test_components() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_my_writable_repositories_with_failing_tool_tests() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_my_writable_repositories_with_install_errors() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_my_writable_repositories_with_invalid_tools() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_my_writable_repositories_with_no_failing_tool_tests() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method)

browse_my_writable_repositories_with_skip_tool_test_checked() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.admin.AdminController method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_by_user() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_i_can_administer() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_i_own() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_in_category() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_missing_tool_test_components() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_with_failing_tool_tests() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_with_install_errors() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_with_invalid_tools() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_with_no_failing_tool_tests() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_with_skip_tool_test_checked() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repository_dependencies() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repository_metadata() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) browse_request_types() (galaxy.webapps.galaxy.controllers.request_type.RequestType method) browse_requests() (galaxy.webapps.galaxy.controllers.requests.Requests method) (galaxy.webapps.galaxy.controllers.requests_admin.RequestsAdmin method) browse_review() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) browse_tool_dependencies() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_tool_dependency() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) browse_tool_shed() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) browse_tool_sheds() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) browse_tools() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_valid_categories() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_valid_repositories() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browser_url (galaxy.web.framework.base.Request attribute) bucket_proxy() (galaxy.webapps.galaxy.controllers.root.RootController method) build() (galaxy.tools.parameters.basic.ToolParameter class method) build_approved_select_field() (in module tool_shed.grids.util) build_changeset_revision_select_field() (in module tool_shed.grids.util) build_command_line() (galaxy.jobs.runners.BaseJobRunner method) build_dependency_manager() (in module galaxy.tools.deps) build_dependency_shell_commands() (galaxy.tools.Tool method) build_dir (galaxy.eggs.scramble.ScrambleEgg attribute) build_form_definition_field_widgets() (galaxy.webapps.galaxy.controllers.forms.Forms method) build_form_id_select_field() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) build_from_current_history() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) build_index() (galaxy.tools.search.ToolBoxSearch method) build_initial_query() (galaxy.web.framework.helpers.grids.Grid method) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid method) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid method) (galaxy.webapps.galaxy.controllers.forms.FormsGrid method) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid method) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid method) (galaxy.webapps.galaxy.controllers.library.LibraryListGrid method) (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid method) (galaxy.webapps.galaxy.controllers.user.UserOpenIDGrid method) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid method) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid method) (tool_shed.grids.admin_grids.AdminRepositoryGrid method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid method) (tool_shed.grids.repository_grids.DatatypesGrid method) (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithFailingToolTestsGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithNoFailingToolTestsGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithSkipTestsCheckedGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithTestInstallErrorsGrid method) (tool_shed.grids.repository_grids.RepositoriesByUserGrid method) (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid method) (tool_shed.grids.repository_grids.RepositoriesIOwnGrid method) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid method) (tool_shed.grids.repository_grids.RepositoriesMissingToolTestComponentsGrid method) (tool_shed.grids.repository_grids.RepositoriesWithFailingToolTestsGrid method) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid method) (tool_shed.grids.repository_grids.RepositoriesWithNoFailingToolTestsGrid method) (tool_shed.grids.repository_grids.RepositoriesWithSkipTestsCheckedGrid method) (tool_shed.grids.repository_grids.RepositoriesWithTestInstallErrorsGrid method) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid method) (tool_shed.grids.repository_grids.RepositoryGrid method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid method) (tool_shed.grids.repository_grids.ToolDependenciesGrid method) (tool_shed.grids.repository_grids.ToolsGrid method) (tool_shed.grids.repository_grids.ValidRepositoryGrid method) (tool_shed.grids.repository_review_grids.RepositoriesReadyForReviewGrid method) (tool_shed.grids.repository_review_grids.RepositoriesReviewedByMeGrid method) (tool_shed.grids.repository_review_grids.RepositoriesWithNoToolTestsGrid method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid method) (tool_shed.grids.repository_review_grids.RepositoriesWithoutReviewsGrid method) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid method) (tool_shed.grids.repository_review_grids.ReviewedRepositoriesIOwnGrid method) build_invocations_query() (galaxy.managers.workflows.WorkflowsManager method) build_maf_index() (in module galaxy.tools.util.maf_utilities) build_maf_index_species_chromosomes() (in module galaxy.tools.util.maf_utilities) build_module() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) build_object_store_from_config() (in module galaxy.objectstore) build_parameter_dict() (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) build_path() (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method) build_readme_files_dict() (in module tool_shed.util.readme_util) build_redirect_url_params() (galaxy.tools.Tool method) build_rename_datasets_for_sample_select_field() (in module galaxy.webapps.galaxy.controllers.requests_admin) build_select_field() (in module galaxy.web.form_builder) build_shed_tool_conf_select_field() (in module tool_shed.util.tool_util) build_template() (galaxy.external_services.actions.Template method) build_template_error_formatters() (in module galaxy.webapps.reports.buildapp) (in module galaxy.webapps.tool_shed.buildapp) build_tool_dependencies_select_field() (in module tool_shed.util.tool_dependency_util) build_tool_panel_section_select_field() (in module tool_shed.util.tool_util) build_url() (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) build_workflow_from_dict() (galaxy.managers.workflows.WorkflowContentsManager method) bulk_operations (galaxy.model.Sample attribute) Bunch (class in galaxy.util.bunch) by_id() (galaxy.managers.base.ModelManager method) by_ids() (galaxy.managers.base.ModelManager method) by_user() (galaxy.managers.histories.HistoryManager method)

C

cache_job_destination() (galaxy.jobs.mapper.JobRunnerMapper method) CacheableStaticURLParser (class in galaxy.web.framework.middleware.static) CachingObjectStore (class in galaxy.objectstore) calculate_disk_usage() (galaxy.model.User method) call_hook() (galaxy.tools.Tool method) camelize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) can_access_dataset() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_access_library() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_access_library_item() (galaxy.security.GalaxyRBACAgent method) can_access_request_type() (galaxy.security.GalaxyRBACAgent method) can_add() (pkg_resources.Environment method) can_add_item() (galaxy.managers.folders.FolderManager method) can_add_library_item() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_browse_repository_reviews() (in module tool_shed.util.review_util) can_change_type() (galaxy.webapps.tool_shed.model.Repository method) can_change_type_to() (galaxy.webapps.tool_shed.model.Repository method) can_convert_to() (galaxy.model.DatasetInstance method) can_current_user_add_to_library_item() (galaxy.web.base.controller.UsesLibraryMixinItems method) can_manage_dataset() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_manage_library_item() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_modify_library_item() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_push() (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) can_split() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) CANCEL (galaxy.web.framework.openid_manager.OpenIDManager attribute) cancel() (galaxy.model.WorkflowInvocation method) cancel_invocation() (galaxy.managers.workflows.WorkflowsManager method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) CancelWorkflowEvaluation CaseSensitiveConfigParser (class in galaxy.eggs) categories (galaxy.webapps.tool_shed.model.Repository attribute) Category (class in galaxy.webapps.tool_shed.model) category (galaxy.webapps.tool_shed.model.RepositoryCategoryAssociation attribute) category_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) category_id (galaxy.webapps.tool_shed.model.RepositoryCategoryAssociation attribute) CategoryGrid (class in tool_shed.grids.repository_grids) CategoryGrid.DescriptionColumn (class in tool_shed.grids.repository_grids) CategoryGrid.NameColumn (class in tool_shed.grids.repository_grids) CategoryGrid.RepositoriesColumn (class in tool_shed.grids.repository_grids) center() (galaxy.web.base.controllers.admin.Admin method) change_adapter() (galaxy_utils.sequence.fastq.fastqCSSangerRead method) change_datatype() (galaxy.datatypes.registry.Registry method) (galaxy.model.DatasetInstance method) change_entry() (galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager method) change_ownership_for_run() (galaxy.jobs.JobWrapper method) change_password() (galaxy.webapps.galaxy.controllers.user.User method) change_state() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) ChangeDatatypeAction (class in galaxy.jobs.actions.post) changeset_revision (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) changeset_revision_reviewed_by_user() (in module tool_shed.util.review_util) check() (galaxy.config.Configuration method) (galaxy.webapps.reports.config.Configuration method) (galaxy.webapps.tool_shed.config.Configuration method) check_accessible() (galaxy.managers.folders.FolderManager method) (galaxy.managers.libraries.LibraryManager method) check_and_reload() (galaxy.visualization.genomes.Genomes method) check_and_update_param_values() (galaxy.tools.Tool method) check_and_update_param_values_helper() (galaxy.tools.Tool method) check_and_update_state() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) check_binary() (in module galaxy.datatypes.checkers) check_bz2() (in module galaxy.datatypes.checkers) check_conditional() (galaxy.eggs.GalaxyConfig method) check_folder_contents() (galaxy.security.GalaxyRBACAgent method) check_for_missing_tools() (in module tool_shed.util.common_util) check_for_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) check_for_updates() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) check_gzip() (in module galaxy.datatypes.checkers) check_html() (in module galaxy.datatypes.checkers) check_if_output_datasets_deleted() (galaxy.model.Job method) check_image() (in module galaxy.datatypes.checkers) check_image_type() (in module galaxy.datatypes.util.image_util) check_interval (galaxy.jobs.deferred.data_transfer.DataTransfer attribute) (galaxy.model.DeferredJob attribute) check_job() (galaxy.jobs.deferred.data_transfer.DataTransfer method) (galaxy.jobs.deferred.manual_data_transfer.ManualDataTransferPlugin method) (galaxy.jobs.deferred.pacific_biosciences_smrt_portal.SMRTPortalPlugin method) check_limits() (galaxy.jobs.JobWrapper method) (galaxy.jobs.runners.AsynchronousJobState method) check_manageable() (galaxy.managers.folders.FolderManager method) check_newlines() (in module galaxy.datatypes.sniff) check_param() (in module galaxy.tools.parameters) check_param_from_incoming() (in module galaxy.tools) check_password() (galaxy.model.User method) (galaxy.webapps.tool_shed.model.User method) check_pid() (galaxy.jobs.runners.lwr.LwrJobRunner method) check_security() (galaxy.managers.workflows.WorkflowsManager method) check_tool_output() (galaxy.jobs.JobWrapper method) check_tool_tag_set() (in module tool_shed.util.common_util) check_user_can_add_to_library_item() (galaxy.web.base.controller.UsesLibraryMixinItems method) check_version_conflict() (pkg_resources.Distribution method) check_watched_item() (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.jobs.runners.lwr.LwrJobRunner method) check_watched_items() (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.condor.CondorJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) check_workflow_compatible() (galaxy.tools.Tool method) check_zip() (in module galaxy.datatypes.checkers) CheckboxField (class in galaxy.web.form_builder) checkComments() (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) children (galaxy.webapps.tool_shed.model.Tag attribute) chop_block_by_region() (in module galaxy.tools.util.maf_utilities) ChromatinInteractions (class in galaxy.datatypes.interval) ChromInfo (class in galaxy.datatypes.chrominfo) chroms() (galaxy.visualization.genomes.Genomes method) chunk64_dataprovider() (galaxy.datatypes.data.Data method) chunk_dataprovider() (galaxy.datatypes.data.Data method) CHUNKABLE (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.tabular.Tabular attribute) CisML (class in galaxy.datatypes.xml) CitationCollection (class in galaxy.managers.citations) citations() (galaxy.webapps.galaxy.api.histories.HistoriesController method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) citations_for_tool() (galaxy.managers.citations.CitationsManager method) citations_for_tool_ids() (galaxy.managers.citations.CitationsManager method) CitationsManager (class in galaxy.managers.citations) class_type (in module galaxy.external_services.service) classify() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) clean_base_dir() (galaxy.tools.data.TabularToolDataField method) clean_field_contents() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) cleanNewickString() (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method) cleanTag() (galaxy.visualization.data_providers.phyloviz.phyloxmlparser.Phyloxml_Parser method) cleanup() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.jobs.runners.AsynchronousJobState method) cleanup_after_job() (galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper method) (galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper method) cleanup_before_exit() (in module galaxy.datatypes.converters.sam_to_bam) cleanup_external_metadata() (galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper method) cleanup_from_JSON_dict_filename() (galaxy.datatypes.metadata.MetadataTempFile class method) cleanup_resources() (pkg_resources.ResourceManager method) cleanup_unused_precreated_datasets() (in module galaxy.tools.actions.upload_common) clear() (galaxy.model.ImplicitlyConvertedDatasetAssociation method) (galaxy.util.lrucache.LRUCache method) (galaxy.util.odict.odict method) clear_associated_files() (galaxy.model.DatasetInstance method) (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.LibraryDatasetDatasetAssociation method) clear_display_apps() (galaxy.datatypes.data.Data method) clear_history() (galaxy.webapps.galaxy.controllers.root.RootController method) clear_working_directory() (galaxy.jobs.JobWrapper method) clone() (galaxy_utils.sequence.sequence.SequencingRead method) (pkg_resources.Distribution method) close() (galaxy.datatypes.converters.interval_to_coverage.CoverageWriter method) (galaxy.tools.util.maf_utilities.TempFileHandler method) (galaxy_utils.sequence.fasta.fastaNamedReader method) (galaxy_utils.sequence.fasta.fastaReader method) (galaxy_utils.sequence.fasta.fastaWriter method) (galaxy_utils.sequence.fastq.fastqFakeFastaScoreReader method) (galaxy_utils.sequence.fastq.fastqNamedReader method) (galaxy_utils.sequence.fastq.fastqReader method) (galaxy_utils.sequence.fastq.fastqWriter method) cls (in module galaxy.tools.data) coerce() (galaxy.model.custom_types.MutationDict class method) (galaxy.model.custom_types.MutationList class method) (galaxy.model.custom_types.MutationObj class method) col (galaxy.webapps.galaxy.controllers.requests_admin.AdminRequestsGrid attribute) (tool_shed.grids.admin_grids.ManageCategoryGrid attribute) (tool_shed.grids.repository_grids.InstallMatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithNoFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithSkipTestsCheckedGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithTestInstallErrorsGrid attribute) collect_child_datasets() (galaxy.tools.Tool method) collect_dynamic_collections() (galaxy.tools.Tool method) collect_input_dataset_collections() (galaxy.tools.actions.DefaultToolAction method) collect_input_datasets() (galaxy.tools.actions.DefaultToolAction method) collect_primary_datasets() (galaxy.tools.Tool method) collection_type (galaxy.tools.parameters.basic.DataCollectionToolParameter attribute) (galaxy.workflow.modules.InputDataCollectionModule attribute) color_dict (galaxy_utils.sequence.transform.ColorSpaceConverter attribute) color_space_converter (galaxy_utils.sequence.sequence.SequencingRead attribute) color_to_base_dict (galaxy_utils.sequence.transform.ColorSpaceConverter attribute) ColorSpaceConverter (class in galaxy_utils.sequence.transform) ColorToolParameter (class in galaxy.tools.parameters.basic) column_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.Tabular method) column_names (galaxy.datatypes.interval.ChromatinInteractions attribute) (galaxy.datatypes.interval.ENCODEPeak attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Gff3 attribute) (galaxy.datatypes.interval.Gtf attribute) (galaxy.datatypes.tabular.Vcf attribute) column_spec_to_index() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) ColumnDataProvider (class in galaxy.visualization.data_providers.basic) ColumnListParameter (class in galaxy.tools.parameters.basic) ColumnParameter (class in galaxy.datatypes.metadata) ColumnReplaceFilter (class in galaxy.tools.parameters.output) columns (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid attribute) (galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.library.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.HistoryDatasetAssociationSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.HistorySelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.VisualizationSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.WorkflowSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid attribute) (galaxy.webapps.galaxy.controllers.requests_admin.AdminRequestsGrid attribute) (galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid attribute) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid attribute) (galaxy.webapps.galaxy.controllers.user.UserOpenIDGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid attribute) (tool_shed.grids.admin_grids.AdminRepositoryGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.ManageCategoryGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.DatatypesGrid attribute) (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.DockerImageGrid attribute) (tool_shed.grids.repository_grids.EmailAlertsRepositoryGrid attribute) (tool_shed.grids.repository_grids.InstallMatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithNoFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithSkipTestsCheckedGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithTestInstallErrorsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid attribute) (tool_shed.grids.repository_grids.RepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithNoFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithSkipTestsCheckedGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithTestInstallErrorsGrid attribute) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ToolDependenciesGrid attribute) (tool_shed.grids.repository_grids.ToolsGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_grids.ValidRepositoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesReadyForReviewGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesReviewedByMeGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithNoToolTestsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithoutReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) (tool_shed.grids.repository_review_grids.ReviewedRepositoriesIOwnGrid attribute) ColumnSetAction (class in galaxy.jobs.actions.post) ColumnStripFilter (class in galaxy.tools.parameters.output) ColumnTypesParameter (class in galaxy.datatypes.metadata) combine() (galaxy_utils.sequence.fastq.fastqCombiner method) commaify() (in module galaxy.util) commands_in_new_shell (galaxy.jobs.JobWrapper attribute) comment (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.SkipToolTest attribute) commit() (galaxy.model.orm.logging_connection_proxy.LoggingProxy method) CommunityRatingColumn (class in galaxy.web.framework.helpers.grids)

CommunityRBACAgent (class in galaxy.webapps.tool_shed.security) CommunityTagManager (class in galaxy.managers.tags) CommunityTagsColumn (class in galaxy.web.framework.helpers.grids) CommunityWebApplication (class in galaxy.webapps.tool_shed.buildapp) compare_endswith() (in module galaxy.tools.parameters.output) compare_eq() (in module galaxy.tools.parameters.output) compare_gt() (in module galaxy.tools.parameters.output) compare_gte() (in module galaxy.tools.parameters.output) compare_in() (in module galaxy.tools.parameters.output) compare_lt() (in module galaxy.tools.parameters.output) compare_lte() (in module galaxy.tools.parameters.output) compare_neq() (in module galaxy.tools.parameters.output) compare_re_search() (in module galaxy.tools.parameters.output) compare_startswith() (in module galaxy.tools.parameters.output) compare_urls() (in module galaxy.util) compare_values() (galaxy.model.custom_types.JSONType method) compatible_platforms() (in module pkg_resources) complement() (galaxy_utils.sequence.fastq.fastqCSSangerRead method) (galaxy_utils.sequence.sequence.SequencingRead method) Component (class in galaxy.webapps.tool_shed.model) component (galaxy.webapps.tool_shed.model.ComponentReview attribute) component_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) component_id (galaxy.webapps.tool_shed.model.ComponentReview attribute) component_overlaps_region() (in module galaxy.tools.util.maf_utilities) component_reviews (galaxy.webapps.tool_shed.model.RepositoryReview attribute) ComponentGrid (class in tool_shed.grids.repository_review_grids) ComponentGrid.DescriptionColumn (class in tool_shed.grids.repository_review_grids) ComponentGrid.NameColumn (class in tool_shed.grids.repository_review_grids) ComponentReview (class in galaxy.webapps.tool_shed.model) components_are_associated() (galaxy.security.RBACAgent method) composite_files (galaxy.datatypes.data.Data attribute) composite_type (galaxy.datatypes.assembly.Velvet attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.genetics.RexpBase attribute) (galaxy.datatypes.genetics.Rgenetics attribute) (galaxy.datatypes.ngsindex.BowtieIndex attribute) compressed (galaxy.datatypes.binary.CompressedArchive attribute) CompressedArchive (class in galaxy.datatypes.binary) compute_fasta_length() (in module galaxy.datatypes.converters.fasta_to_len) compute_outputs() (galaxy.jobs.JobWrapper method) compute_runtime_state() (galaxy.workflow.modules.SimpleWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) ComputeEnvironment (class in galaxy.jobs) cond_plural() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) Conditional (class in galaxy.tools.parameters.grouping) ConditionalWhen (class in galaxy.tools.parameters.grouping) CondorJobRunner (class in galaxy.jobs.runners.condor) config_directory() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SimpleComputeEnvironment method) config_eggs (galaxy.eggs.Crate attribute) config_exception() (in module galaxy.jobs) config_file (galaxy.eggs.Crate attribute) config_missing (galaxy.eggs.Crate attribute) config_names (galaxy.eggs.Crate attribute) ConfigDoesNotAllowException Configuration (class in galaxy.config) (class in galaxy.webapps.reports.config) (class in galaxy.webapps.tool_shed.config) ConfigurationController (class in galaxy.webapps.galaxy.api.configuration) ConfigurationError, [1], [2], [3] configure_and_load() (galaxy.tools.data.TabularToolDataTable method) configure_logging() (in module galaxy.config) (in module galaxy.webapps.reports.config) (in module galaxy.webapps.tool_shed.config) configure_menu() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) ConfiguresGalaxyMixin (class in galaxy.config) Conflict consume_read() (galaxy_utils.sequence.fastq.fastqAggregator method) contact_owner() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) content (galaxy.external_services.actions.ExternalServiceResult attribute) (galaxy.external_services.actions.ExternalServiceValueResult attribute) (galaxy.external_services.actions.ExternalServiceWebAPIActionResult attribute) contents_iter() (galaxy.model.History method) controller_name (galaxy.webapps.galaxy.api.annotations.HistoryAnnotationsController attribute) (galaxy.webapps.galaxy.api.annotations.HistoryContentAnnotationsController attribute) (galaxy.webapps.galaxy.api.annotations.WorkflowAnnotationsController attribute) (galaxy.webapps.galaxy.api.extended_metadata.HistoryDatasetExtendMetadataController attribute) (galaxy.webapps.galaxy.api.extended_metadata.LibraryDatasetExtendMetadataController attribute) (galaxy.webapps.galaxy.api.item_tags.HistoryContentTagsController attribute) (galaxy.webapps.galaxy.api.item_tags.HistoryTagsController attribute) (galaxy.webapps.galaxy.api.item_tags.WorkflowTagsController attribute) (galaxy.webapps.galaxy.api.provenance.HDAProvenanceController attribute) (galaxy.webapps.galaxy.api.provenance.LDDAProvenanceController attribute) ControllerUnavailable conversion_messages (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) convert_base_to_color_space() (galaxy_utils.sequence.fastq.fastqSequencingRead class method) convert_bed_coords_to_gff() (in module galaxy.datatypes.util.gff_util) convert_bytes() (in module galaxy.objectstore) convert_color_to_base_space() (galaxy_utils.sequence.fastq.fastqSequencingRead class method) convert_dataset() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) convert_gff_coords_to_bed() (in module galaxy.datatypes.util.gff_util) convert_legacy_destinations() (galaxy.jobs.JobConfiguration method) convert_newlines() (in module galaxy.datatypes.sniff) convert_newlines_sep2tabs() (in module galaxy.datatypes.sniff) convert_permitted_action_strings() (galaxy.security.RBACAgent method) (galaxy.webapps.tool_shed.security.RBACAgent method) convert_read_to_format() (galaxy_utils.sequence.fastq.fastqSequencingRead method) convert_score_phred_to_solexa() (galaxy_utils.sequence.fastq.fastqSequencingRead class method) convert_score_solexa_to_phred() (galaxy_utils.sequence.fastq.fastqSequencingRead class method) converter_safe() (galaxy.tools.parameters.basic.DataToolParameter method) ConverterDependencyException converters() (galaxy.webapps.galaxy.api.datatypes.DatatypesController method) cookies (galaxy.web.framework.base.Request attribute) copy() (galaxy.datatypes.util.gff_util.GFFFeature method) (galaxy.datatypes.util.gff_util.GFFInterval method) (galaxy.managers.base.ModelManager method) (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.managers.hdas.HDAManager method) (galaxy.managers.histories.HistoryManager method) (galaxy.model.DatasetCollection method) (galaxy.model.History method) (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.HistoryDatasetCollectionAssociation method) (galaxy.model.ItemTagAssociation method) (galaxy.model.LibraryDatasetDatasetAssociation method) (galaxy.model.Visualization method) (galaxy.model.VisualizationRevision method) (galaxy.tools.DefaultToolState method) (galaxy.util.odict.odict method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) copy_build_script() (galaxy.eggs.scramble.ScrambleEgg method) copy_dataset_permissions() (galaxy.security.GalaxyRBACAgent method) copy_datasets() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) copy_hda_to_library_folder() (galaxy.web.base.controller.UsesLibraryMixinItems method) copy_item_annotation() (galaxy.model.item_attrs.UsesAnnotations method) copy_ldda() (galaxy.managers.hdas.HDAManager method) copy_library_permissions() (galaxy.security.GalaxyRBACAgent method) copy_review() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) copy_safe_peek (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.images.Gmaj attribute) (galaxy.datatypes.images.Laj attribute) copy_sample_file() (in module tool_shed.util.tool_util) copy_sample_files() (in module tool_shed.util.tool_util) copy_tags_from() (galaxy.model.History method) (galaxy.model.StoredWorkflow method) copy_to_collection() (galaxy.model.DatasetCollectionElement method) copy_value() (galaxy.model.custom_types.JSONType method) count_data_lines() (galaxy.datatypes.data.Text method) CoverageWriter (class in galaxy.datatypes.converters.interval_to_coverage) Crate (class in galaxy.eggs) create() (galaxy.managers.base.ModelManager method) (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.managers.folders.FolderManager method) (galaxy.managers.hdas.HDAManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.HierarchicalObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method) (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method) (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController method) (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method) (galaxy.webapps.galaxy.api.folders.FoldersController method) (galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController method) (galaxy.webapps.galaxy.api.groups.GroupAPIController method) (galaxy.webapps.galaxy.api.histories.HistoriesController method) (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method) (galaxy.webapps.galaxy.api.job_files.JobFilesAPIController method) (galaxy.webapps.galaxy.api.jobs.JobController method) (galaxy.webapps.galaxy.api.libraries.LibrariesController method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.metrics.MetricsController method) (galaxy.webapps.galaxy.api.page_revisions.PageRevisionsController method) (galaxy.webapps.galaxy.api.pages.PagesController method) (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method) (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method) (galaxy.webapps.galaxy.api.request_types.RequestTypeAPIController method) (galaxy.webapps.galaxy.api.roles.RoleAPIController method) (galaxy.webapps.galaxy.api.search.SearchController method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.user.User method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method) create_api_key() (galaxy.managers.api_keys.ApiKeyManager method) (galaxy.web.base.controller.CreatesApiKeysMixin method) create_applet_tag_peek() (in module galaxy.datatypes.images) create_archive() (in module galaxy.tools.imp_exp.export_history) create_category() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) create_changeset_revision() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method) create_component() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) create_dataset_collection() (galaxy.managers.collections.DatasetCollectionManager method) create_display() (galaxy.webapps.galaxy.controllers.ucsc_proxy.UCSCProxy method) create_extended_metadata() (galaxy.web.base.controller.UsesExtendedMetadataMixin method) create_external_service() (galaxy.webapps.galaxy.controllers.external_service.ExternalService method) create_folder() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) create_form_definition() (galaxy.webapps.galaxy.controllers.forms.Forms method) create_galaxy_docker_image() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) create_group() (galaxy.web.base.controllers.admin.Admin method) create_item_slug() (galaxy.web.base.controller.SharableMixin method) create_job() (galaxy.jobs.deferred.data_transfer.DataTransfer method) (galaxy.jobs.deferred.manual_data_transfer.ManualDataTransferPlugin method) (galaxy.jobs.deferred.pacific_biosciences_smrt_portal.SMRTPortalPlugin method) (in module galaxy.tools.actions.upload_common) create_library() (galaxy.webapps.galaxy.controllers.library_admin.LibraryAdmin method) create_new_current() (galaxy.webapps.galaxy.controllers.history.HistoryController method) create_new_user() (galaxy.web.base.controllers.admin.Admin method) create_object_in_session() (in module galaxy.objectstore) create_or_update_tool_dependency() (in module tool_shed.util.tool_dependency_util) create_or_update_tool_shed_repository() (in module tool_shed.util.shed_util_common) create_or_verify_database() (in module galaxy.model.migrate.check) (in module galaxy.webapps.tool_shed.model.migrate.check) create_paramfile() (in module galaxy.tools.actions.upload_common) create_private_user_role() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) (galaxy.webapps.tool_shed.security.RBACAgent method) create_quota() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) create_repository() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) create_request() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) create_request_type() (galaxy.webapps.galaxy.controllers.request_type.RequestType method) create_review() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) create_role() (galaxy.web.base.controllers.admin.Admin method) create_time (galaxy.webapps.tool_shed.model.APIKeys attribute) (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.GalaxySession attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.SkipToolTest attribute) (galaxy.webapps.tool_shed.model.User attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) create_tool() (galaxy.tools.ToolBox method) create_tool_dependency_objects() (in module tool_shed.util.tool_dependency_util) create_user() (galaxy.web.base.controller.CreatesUsersMixin method) create_visualization() (galaxy.web.base.controller.UsesVisualizationMixin method) create_working_directory() (galaxy.jobs.JobWrapper method) CreatedWorkflow (class in galaxy.managers.workflows) CreatesApiKeysMixin (class in galaxy.web.base.controller) CreatesUsersMixin (class in galaxy.web.base.controller) creating_job (galaxy.model.DatasetInstance attribute) csFasta (class in galaxy.datatypes.sequence) css() (in module galaxy.web.framework.helpers) cur_filter_pref_name (galaxy.web.framework.helpers.grids.Grid attribute) cur_sort_key_pref_name (galaxy.web.framework.helpers.grids.Grid attribute) current_history_json() (galaxy.webapps.galaxy.controllers.history.HistoryController method) cursor_execute() (galaxy.model.orm.logging_connection_proxy.LoggingProxy method) (galaxy.model.orm.logging_connection_proxy.TraceLoggerProxy method) CustomTrack (class in galaxy.datatypes.interval) cut_and_decode() (galaxy.managers.folders.FolderManager method) cut_the_prefix() (galaxy.managers.folders.FolderManager method) CycleError

D

Data (class in galaxy.datatypes.data) data_conversion_status() (galaxy.managers.hdas.HDAManager method) data_source_redirect() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) data_sources (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.BigBed attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.BedGraph attribute) (galaxy.datatypes.interval.ChromatinInteractions attribute) (galaxy.datatypes.interval.ENCODEPeak attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.tabular.Vcf attribute) data_transfer (in module galaxy.sample_tracking.data_transfer) data_transfer_protocol (galaxy.model.ExternalService attribute) DataCollectionToolParameter (class in galaxy.tools.parameters.basic) DataDestinationTool (class in galaxy.tools) DataManagerHistoryAssociation (class in galaxy.model) DataManagerJobAssociation (class in galaxy.model) DataManagerTool (class in galaxy.tools) DataMeta (class in galaxy.datatypes.data) DataMetaFilter (class in galaxy.tools.parameters.dynamic_options) dataprovider() (galaxy.datatypes.data.Data method) dataproviders (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.tabular.Tabular attribute) (galaxy.datatypes.tabular.Vcf attribute) (galaxy.datatypes.xml.GenericXml attribute) Dataset (class in galaxy.model) dataset (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.JobExternalOutputMetadata attribute) dataset_access_mapping() (galaxy.security.GalaxyRBACAgent method) dataset_collectors (galaxy.tools.ToolOutputCollection attribute) dataset_column_dataprovider() (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.Tabular method) dataset_content_needs_grooming() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.data.Data method) dataset_datatype_re (galaxy.jobs.deferred.data_transfer.DataTransfer attribute) dataset_detail() (galaxy.webapps.galaxy.controllers.mobile.Mobile method) dataset_dict_dataprovider() (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.Tabular method) dataset_elements (galaxy.model.DatasetCollection attribute) dataset_info() (galaxy.webapps.reports.controllers.system.System method) dataset_instance (galaxy.model.DatasetCollectionElement attribute) dataset_instances (galaxy.model.DatasetCollection attribute) dataset_is_private_to_user() (galaxy.security.GalaxyRBACAgent method) dataset_is_public() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) dataset_is_unrestricted() (galaxy.security.GalaxyRBACAgent method) dataset_make_primary() (galaxy.webapps.galaxy.controllers.root.RootController method) dataset_name_re (galaxy.jobs.deferred.data_transfer.DataTransfer attribute) dataset_peek() (galaxy.webapps.galaxy.controllers.mobile.Mobile method) dataset_permission_map_for_access() (galaxy.security.GalaxyRBACAgent method) dataset_transfer_status_updates() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) dataset_type (galaxy.visualization.data_providers.phyloviz.PhylovizDataProvider attribute) DatasetCollection (class in galaxy.model) DatasetCollectionElement (class in galaxy.model) DatasetCollectionInstance (class in galaxy.model) DatasetCollectionManager (class in galaxy.managers.collections) DatasetCollectionsController (class in galaxy.webapps.galaxy.api.dataset_collections) DatasetInstance (class in galaxy.model) DatasetInterface (class in galaxy.webapps.galaxy.controllers.dataset) DatasetOkValidator (class in galaxy.tools.parameters.validation) DatasetPermissions (class in galaxy.model) datasets_are_public() (galaxy.security.GalaxyRBACAgent method) datasets_for_lddas() (in module galaxy.webapps.galaxy.controllers.library_common) DatasetTagAssociation (class in galaxy.model) DatasetToValidationErrorAssociation (class in galaxy.model) DataSourceTool (class in galaxy.tools) DataToolParameter (class in galaxy.tools.parameters.basic) DataTransfer (class in galaxy.jobs.deferred.data_transfer) DataTransferFactory (class in galaxy.sample_tracking.data_transfer) DataTransferGrid (class in galaxy.webapps.galaxy.controllers.requests_admin) DataTransferGrid.ExternalServiceColumn (class in galaxy.webapps.galaxy.controllers.requests_admin) DataTransferGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.requests_admin) DataTransferGrid.SizeColumn (class in galaxy.webapps.galaxy.controllers.requests_admin) DataTransferGrid.StatusColumn (class in galaxy.webapps.galaxy.controllers.requests_admin) datatx_grid (galaxy.webapps.galaxy.controllers.requests_admin.RequestsAdmin attribute) Datatype (class in galaxy.web.base.controller) datatype (galaxy.model.DatasetInstance attribute) DatatypeIsInstanceToolOutputActionConditionalWhen (class in galaxy.tools.parameters.output) datatypes_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) DatatypesController (class in galaxy.webapps.galaxy.api.datatypes) DatatypesGrid (class in tool_shed.grids.repository_grids) DatatypesGrid.DatatypesColumn (class in tool_shed.grids.repository_grids) DateTimeColumn (class in galaxy.web.framework.helpers.grids) db_builds (galaxy.managers.context.ProvidesHistoryContext attribute) db_dataset_for() (galaxy.jobs.deferred.FakeTrans method) (galaxy.managers.context.ProvidesHistoryContext method) db_next_hid() (in module galaxy.model.mapping) dbkey (galaxy.model.DatasetInstance attribute) DBKeyParameter (class in galaxy.datatypes.metadata) dbkeys() (galaxy.webapps.galaxy.controllers.user.User method) deactivate_or_uninstall_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) debugging (galaxy.webapps.galaxy.api.metrics.MetricsController attribute) declare_namespace() (in module pkg_resources) decode() (galaxy.tools.DefaultToolState method) decode_dataset_user() (in module galaxy.datatypes.display_applications.util) decode_dbkey() (in module galaxy.visualization.genomes) decode_folder_id() (galaxy.managers.folders.FolderManager method) decode_guid() (galaxy.web.security.SecurityHelper method) decode_id() (galaxy.web.base.controller.BaseController method) (galaxy.web.security.SecurityHelper method) decode_runtime_state() (galaxy.workflow.modules.SimpleWorkflowModule method) default() (galaxy.webapps.galaxy.controllers.async.ASync method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.root.RootController method) (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) default_collection_type (galaxy.workflow.modules.InputDataCollectionModule attribute) default_compute_environment() (galaxy.jobs.JobWrapper method) default_deserializer() (galaxy.managers.base.ModelDeserializer method) default_exit_code_file() (galaxy.jobs.runners.JobState static method) default_filter (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid attribute) (galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.library.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid attribute) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid attribute) (galaxy.webapps.galaxy.controllers.user.UserOpenIDGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.admin_grids.AdminRepositoryGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) DEFAULT_INVALID_CHAR (galaxy.tools.parameters.sanitize.ToolParameterSanitizer attribute) default_job_file() (galaxy.jobs.runners.JobState static method) default_job_tool_configuration (galaxy.jobs.JobConfiguration attribute) DEFAULT_MAX_OPEN_FILES (galaxy.tools.util.maf_utilities.TempFileHandler attribute) default_name (galaxy.model.History attribute) (galaxy.workflow.modules.InputDataCollectionModule attribute) (galaxy.workflow.modules.InputDataModule attribute) (galaxy.workflow.modules.PauseModule attribute) DEFAULT_NWORKERS (galaxy.jobs.JobConfiguration attribute) default_printer() (in module galaxy.tools.util.galaxyops) default_quota (galaxy.quota.NoQuotaAgent attribute) default_registered_quota (galaxy.quota.QuotaAgent attribute) default_serializer() (galaxy.managers.base.ModelSerializer method) default_sort_key (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid attribute) (galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.library.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid attribute) (galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid attribute) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid attribute) (galaxy.webapps.galaxy.controllers.user.UserOpenIDGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.DatatypesGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ToolDependenciesGrid attribute) (tool_shed.grids.repository_grids.ToolsGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) DEFAULT_SPECS (galaxy.jobs.runners.BaseJobRunner attribute) default_state() (galaxy.workflow.modules.InputDataCollectionModule class method) (galaxy.workflow.modules.InputDataModule class method) (galaxy.workflow.modules.PauseModule class method) (galaxy.workflow.modules.SimpleWorkflowModule class method) default_template (galaxy.tools.Tool attribute) default_tool_action (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.Tool attribute) default_unregistered_quota (galaxy.quota.QuotaAgent attribute) DEFAULT_VALUE_MAP() (in module galaxy.tools.parameters.basic) DefaultHistoryPermissions (class in galaxy.model) DefaultJobAction (class in galaxy.jobs.actions.post) DefaultJobDispatcher (class in galaxy.jobs.handler) DefaultProvider (class in pkg_resources) DefaultQuotaAssociation (class in galaxy.model) DefaultToolAction (class in galaxy.tools.actions) DefaultToolState (class in galaxy.tools) DefaultUserPermissions (class in galaxy.model) DefaultWebTransaction (class in galaxy.web.framework.base) DeferredJob (class in galaxy.model) DeferredJobQueue (class in galaxy.jobs.deferred) DelayedWorkflowEvaluation

delete() (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.managers.folders.FolderManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method) (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController method) (galaxy.webapps.galaxy.api.folders.FoldersController method) (galaxy.webapps.galaxy.api.group_roles.GroupRolesAPIController method) (galaxy.webapps.galaxy.api.group_users.GroupUsersAPIController method) (galaxy.webapps.galaxy.api.histories.HistoriesController method) (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method) (galaxy.webapps.galaxy.api.lda_datasets.LibraryDatasetsController method) (galaxy.webapps.galaxy.api.libraries.LibrariesController method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.pages.PagesController method) (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method) (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method) (galaxy.webapps.galaxy.api.tool_data.ToolData method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) delete_address() (galaxy.webapps.galaxy.controllers.user.User method) delete_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) delete_current() (galaxy.webapps.galaxy.controllers.history.HistoryController method) delete_extended_metadata() (galaxy.web.base.controller.UsesExtendedMetadataMixin method) delete_external_service() (galaxy.webapps.galaxy.controllers.external_service.ExternalService method) delete_external_service_associations() (galaxy.model.RequestType method) delete_form_definition() (galaxy.webapps.galaxy.controllers.forms.Forms method) delete_hidden_datasets() (galaxy.webapps.galaxy.controllers.history.HistoryController method) delete_item_annotation() (galaxy.model.item_attrs.UsesAnnotations method) delete_item_tags() (galaxy.managers.tags.TagManager method) delete_library() (galaxy.webapps.galaxy.controllers.library_admin.LibraryAdmin method) delete_library_item() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) delete_operation (galaxy.web.base.controllers.admin.Admin attribute) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) delete_repository() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) delete_repository_metadata() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) delete_request() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) delete_request_type() (galaxy.webapps.galaxy.controllers.request_type.RequestType method) delete_sample() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) delete_template() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) deleted (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.User attribute) deleted_datasets() (galaxy.webapps.reports.controllers.system.System method) deleted_histories() (galaxy.webapps.reports.controllers.system.System method) DeleteDatasetAction (class in galaxy.jobs.actions.post) DeletedColumn (class in galaxy.web.framework.helpers.grids) DeleteIntermediatesAction (class in galaxy.jobs.actions.post) demodulize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) dependency_shell_commands() (galaxy.tools.deps.DependencyManager method) (galaxy.tools.deps.NullDependencyManager method) DependencyManager (class in galaxy.tools.deps) deprecate() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) deprecated (galaxy.webapps.tool_shed.model.Repository attribute) deprecated_options (galaxy.config.Configuration attribute) deprecated_repositories_i_own_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) DeprecatedMethod DeprecatedRepositoriesIOwnGrid (class in tool_shed.grids.repository_grids) derive_roles_from_access() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) description (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.Component attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.Role attribute) deserialize() (galaxy.managers.base.ModelDeserializer method) deserialize_basestring() (galaxy.managers.base.ModelDeserializer method) deserialize_bool() (galaxy.managers.base.ModelDeserializer method) deserialize_genome_build() (galaxy.managers.base.ModelDeserializer method) deserialize_int() (galaxy.managers.base.ModelDeserializer method) determine_output_format() (in module galaxy.tools.actions) dict_collection_visible_keys (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.Group attribute) (galaxy.model.History attribute) (galaxy.model.ItemTagAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.Library attribute) (galaxy.model.Quota attribute) (galaxy.model.Request attribute) (galaxy.model.RequestType attribute) (galaxy.model.Role attribute) (galaxy.model.Sample attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.User attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowRequest attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.tools.Tool attribute) (galaxy.tools.ToolOutput attribute) (galaxy.tools.data.TabularToolDataField attribute) (galaxy.tools.data.TabularToolDataTable attribute) (galaxy.tools.parameters.basic.FloatToolParameter attribute) (galaxy.tools.parameters.basic.IntegerToolParameter attribute) (galaxy.tools.parameters.basic.ToolParameter attribute) (galaxy.tools.parameters.grouping.ConditionalWhen attribute) (galaxy.tools.parameters.grouping.Group attribute) (galaxy.tools.parameters.grouping.Repeat attribute) (galaxy.tools.parameters.grouping.Section attribute) (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.SkipToolTest attribute) (galaxy.webapps.tool_shed.model.User attribute) dict_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.Tabular method) dict_element_visible_keys (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.Group attribute) (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.History attribute) (galaxy.model.ItemTagAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.Page attribute) (galaxy.model.PageRevision attribute) (galaxy.model.Quota attribute) (galaxy.model.RequestType attribute) (galaxy.model.Role attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.User attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowRequest attribute) (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.SkipToolTest attribute) (galaxy.webapps.tool_shed.model.User attribute) Dictifiable (class in galaxy.model.item_attrs) dictify_dataset_collection_instance() (in module galaxy.managers.collections_util) dictify_element() (in module galaxy.managers.collections_util) DictParameter (class in galaxy.datatypes.metadata) directory_hash_id() (in module galaxy.webapps.tool_shed.model) disk_usage() (galaxy.webapps.reports.controllers.system.System method) DiskObjectStore (class in galaxy.objectstore) display() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.root.RootController method) display_amount (galaxy.model.Quota attribute) display_application() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) display_applications() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) display_as() (galaxy.webapps.galaxy.controllers.root.RootController method) display_at() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) display_by_id() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) display_by_username_and_slug() (galaxy.web.base.controller.SharableMixin method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) display_child() (galaxy.webapps.galaxy.controllers.root.RootController method) display_data() (galaxy.datatypes.binary.Binary method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.tabular.Tabular method) display_image_in_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) display_info() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) display_name() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetCollectionInstance method) (galaxy.model.DatasetInstance method) (galaxy.model.LibraryDataset method) display_peek() (galaxy.datatypes.binary.Ab1 method) (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.binary.BigWig method) (galaxy.datatypes.binary.CompressedArchive method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.H5 method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.binary.Scf method) (galaxy.datatypes.binary.Sff method) (galaxy.datatypes.binary.Sra method) (galaxy.datatypes.binary.TwoBit method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.rgTabList method) (galaxy.datatypes.images.Gmaj method) (galaxy.datatypes.images.Laj method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) (galaxy.datatypes.ngsindex.BowtieIndex method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.tabular.Pileup method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.Tabular method) (galaxy.datatypes.tabular.Taxonomy method) (galaxy.datatypes.tabular.Vcf method) (galaxy.model.DatasetInstance method) display_ready() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) display_structured() (galaxy.webapps.galaxy.controllers.history.HistoryController method) display_tool() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) display_url() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) displayable() (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.Tabular method) DisplayApplication (class in galaxy.datatypes.display_applications.application) DisplayApplicationDataParameter (class in galaxy.datatypes.display_applications.parameters) DisplayApplicationLink (class in galaxy.datatypes.display_applications.application) DisplayApplicationParameter (class in galaxy.datatypes.display_applications.parameters) DisplayApplicationTemplateParameter (class in galaxy.datatypes.display_applications.parameters) DisplayByUsernameAndSlugGridOperation (class in galaxy.web.framework.helpers.grids) DisplayDataValueWrapper (class in galaxy.datatypes.display_applications.parameters) DisplayParameterValueWrapper (class in galaxy.datatypes.display_applications.parameters) dist_config_file (galaxy.eggs.dist.DistScrambleCrate attribute) DistributedObjectStore (class in galaxy.objectstore) Distribution (class in pkg_resources) DistributionNotFound DistScrambleCrate (class in galaxy.eggs.dist) DistScrambleEgg (class in galaxy.eggs.dist) DNA_COMPLEMENT (galaxy.tools.util.maf_utilities.RegionAlignment attribute) (galaxy.tools.util.maf_utilities.SplicedAlignment attribute) DNA_complement() (in module galaxy_utils.sequence.transform) DNA_reverse_complement() (in module galaxy_utils.sequence.transform) do_fast_split() (galaxy.datatypes.sequence.Sequence class method) do_invocation_step_action() (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.WorkflowModule method) do_merge() (in module galaxy.jobs.splitters.basic) (in module galaxy.jobs.splitters.multi) do_not_test (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) do_slow_split() (galaxy.datatypes.sequence.Sequence class method) do_split() (in module galaxy.jobs.splitters.basic) (in module galaxy.jobs.splitters.multi) docker_image_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) DockerImageGrid (class in tool_shed.grids.repository_grids) docstring_trim() (in module galaxy.util) doi() (galaxy.managers.citations.DoiCitation method) DoiCache (class in galaxy.managers.citations) DoiCitation (class in galaxy.managers.citations) download() (galaxy.webapps.galaxy.api.lda_datasets.LibraryDatasetsController method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) download_dataset_from_folder() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) download_field_file() (galaxy.webapps.galaxy.api.tool_data.ToolData method) downloadable (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) downloadable_revisions (galaxy.webapps.tool_shed.model.Repository attribute) DrillDownField (class in galaxy.web.form_builder) DrillDownSelectToolParameter (class in galaxy.tools.parameters.basic) DRMAAJobRunner (class in galaxy.jobs.runners.drmaa) DummyDataset (class in galaxy.tools.parameters.basic) dump() (galaxy.util.aliaspickler.AliasPickleModule method) dumps() (galaxy.util.aliaspickler.AliasPickleModule method) (in module galaxy.util.json) DuplicatedIdentifierException DuplicatedSlugException dynamic_structure (galaxy.tools.ToolOutputCollection attribute) dynamic_tool_confs() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method) DynamicDisplayApplicationBuilder (class in galaxy.datatypes.display_applications.application) DynamicOptions (class in galaxy.tools.parameters.dynamic_options)

E

eagers (pkg_resources.ZipProvider attribute) echo() (galaxy.webapps.galaxy.controllers.root.RootController method) echo_json() (galaxy.webapps.galaxy.controllers.root.RootController method) edit() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.page.PageController method) edit_address() (galaxy.webapps.galaxy.controllers.user.User method) edit_basic_request_info() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) edit_category() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) edit_component() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) edit_content() (galaxy.webapps.galaxy.controllers.page.PageController method) edit_email_settings() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) edit_external_service() (galaxy.webapps.galaxy.controllers.external_service.ExternalService method) edit_external_service_form_definition() (galaxy.webapps.galaxy.controllers.external_service.ExternalService method) edit_form_definition() (galaxy.webapps.galaxy.controllers.forms.Forms method) edit_info() (galaxy.webapps.galaxy.controllers.user.User method) edit_quota() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) edit_request_type() (galaxy.webapps.galaxy.controllers.request_type.RequestType method) edit_review() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) edit_samples() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) edit_template() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) edit_template_info() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) edit_toolbox_filters() (galaxy.webapps.galaxy.controllers.user.User method) edit_username() (galaxy.webapps.galaxy.controllers.user.User method) editable_keys (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) editor() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) editor_form_post() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) effective_output_name (galaxy.tools.ToolOutputCollectionPart attribute) Egg (class in galaxy.eggs) egg_info (pkg_resources.NullProvider attribute) egg_name (pkg_resources.NullProvider attribute) egg_name() (pkg_resources.Distribution method) EggMetadata (class in pkg_resources) EggNotFetchable EggProvider (class in pkg_resources) Eigenstratgeno (class in galaxy.datatypes.genetics) Eigenstratpca (class in galaxy.datatypes.genetics) Eland (class in galaxy.datatypes.tabular) ElandMulti (class in galaxy.datatypes.tabular) element_is_set() (galaxy.datatypes.metadata.MetadataCollection method) element_object (galaxy.model.DatasetCollectionElement attribute) element_type (galaxy.model.DatasetCollectionElement attribute) ELEMENTS_UNINITIALIZED (galaxy.managers.collections.DatasetCollectionManager attribute) email (galaxy.webapps.tool_shed.model.User attribute) email_alerts (galaxy.webapps.tool_shed.model.Repository attribute) email_alerts_repository_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) EmailAction (class in galaxy.jobs.actions.post) EmailAlertsRepositoryGrid (class in tool_shed.grids.repository_grids) empty (galaxy.model.History attribute) empty() (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) empty_field (galaxy.webapps.galaxy.controllers.forms.Forms attribute) EmptyProvider (class in pkg_resources) EmptyTextfieldValidator (class in galaxy.tools.parameters.validation) encode() (galaxy.tools.DefaultToolState method) encode_all_ids() (galaxy.web.base.controller.BaseController method) (galaxy.web.security.SecurityHelper method) encode_dataset_user() (in module galaxy.datatypes.display_applications.util) encode_dict_ids() (galaxy.web.security.SecurityHelper method) encode_guid() (galaxy.web.security.SecurityHelper method) encode_id() (galaxy.web.security.SecurityHelper method) encode_runtime_state() (galaxy.workflow.modules.SimpleWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) ENCODEPeak (class in galaxy.datatypes.interval) end (galaxy.tools.util.maf_utilities.SplicedAlignment attribute) engine (galaxy.model.Dataset attribute) English (class in galaxy.util.inflection) ensure_directory() (in module pkg_resources) ensure_tempdir() (galaxy.config.Configuration method) EntryPoint (class in pkg_resources) Environment (class in pkg_resources) Eps (class in galaxy.datatypes.images) equals() (galaxy.managers.citations.BaseCitation method) err_code (galaxy.exceptions.ActionInputError attribute) (galaxy.exceptions.AdminRequiredException attribute) (galaxy.exceptions.AuthenticationFailed attribute) (galaxy.exceptions.AuthenticationRequired attribute) (galaxy.exceptions.ConfigDoesNotAllowException attribute) (galaxy.exceptions.ConfigurationError attribute) (galaxy.exceptions.Conflict attribute) (galaxy.exceptions.DeprecatedMethod attribute) (galaxy.exceptions.DuplicatedIdentifierException attribute) (galaxy.exceptions.DuplicatedSlugException attribute) (galaxy.exceptions.InconsistentDatabase attribute) (galaxy.exceptions.InsufficientPermissionsException attribute) (galaxy.exceptions.InternalServerError attribute) (galaxy.exceptions.ItemAccessibilityException attribute) (galaxy.exceptions.ItemOwnershipException attribute) (galaxy.exceptions.MalformedId attribute) (galaxy.exceptions.MessageException attribute) (galaxy.exceptions.NotImplemented attribute) (galaxy.exceptions.ObjectAttributeInvalidException attribute) (galaxy.exceptions.ObjectAttributeMissingException attribute) (galaxy.exceptions.ObjectNotFound attribute) (galaxy.exceptions.RequestParameterInvalidException attribute) (galaxy.exceptions.RequestParameterMissingException attribute) (galaxy.exceptions.ToolMetaParameterException attribute) (galaxy.exceptions.UnknownContentsType attribute) Error (class in galaxy.webapps.galaxy.controllers.error) error() (galaxy.web.framework.middleware.remoteuser.RemoteUser method) (galaxy.webapps.tool_shed.framework.middleware.remoteuser.RemoteUser method) error_if_uploading() (galaxy.managers.hdas.HDAManager method) errors() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) Eset (class in galaxy.datatypes.genetics)

estimate_file_lines() (galaxy.datatypes.data.Text method) evaluate_marker() (in module pkg_resources) Event (class in galaxy.model) exec_after_process() (galaxy.tools.DataManagerTool method) (galaxy.tools.SetMetadataTool method) (galaxy.tools.Tool method) exec_before_job() (galaxy.tools.DataSourceTool method) (galaxy.tools.OutputParameterJSONTool method) (galaxy.tools.Tool method) execute() (galaxy.jobs.actions.post.ActionBox class method) (galaxy.jobs.actions.post.ChangeDatatypeAction class method) (galaxy.jobs.actions.post.ColumnSetAction class method) (galaxy.jobs.actions.post.DefaultJobAction class method) (galaxy.jobs.actions.post.DeleteDatasetAction class method) (galaxy.jobs.actions.post.DeleteIntermediatesAction class method) (galaxy.jobs.actions.post.EmailAction class method) (galaxy.jobs.actions.post.HideDatasetAction class method) (galaxy.jobs.actions.post.RenameDatasetAction class method) (galaxy.jobs.actions.post.SetMetadataAction class method) (galaxy.jobs.actions.post.TagDatasetAction class method) (galaxy.tools.Tool method) (galaxy.tools.actions.DefaultToolAction method) (galaxy.tools.actions.ToolAction method) (galaxy.tools.actions.history_imp_exp.ExportHistoryToolAction method) (galaxy.tools.actions.history_imp_exp.ImportHistoryToolAction method) (galaxy.tools.actions.metadata.SetMetadataToolAction method) (galaxy.tools.actions.upload.UploadToolAction method) (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) execute_via_app() (galaxy.tools.actions.metadata.SetMetadataToolAction method) ExecutionTimer (class in galaxy.util) exists() (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.HierarchicalObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) exit_code() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) exmeta_item_id (galaxy.webapps.galaxy.api.extended_metadata.HistoryDatasetExtendMetadataController attribute) (galaxy.webapps.galaxy.api.extended_metadata.LibraryDatasetExtendMetadataController attribute) expand_here_template() (in module galaxy.tools.data) expand_user_properties() (galaxy.model.User static method) expiration_time (galaxy.webapps.tool_shed.model.PasswordResetToken attribute) export() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) (galaxy.webapps.tool_shed.api.repository_revisions.RepositoryRevisionsController method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) export_archive() (galaxy.webapps.galaxy.controllers.history.HistoryController method) export_name (galaxy.model.JobExportHistoryArchive attribute) export_to_file() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) export_to_myexp() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) export_via_api() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) exported_workflows() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) ExportHistoryTool (class in galaxy.tools) ExportHistoryToolAction (class in galaxy.tools.actions.history_imp_exp) ExportsHistoryMixin (class in galaxy.web.base.controller) exposed (galaxy.web.framework.helpers.grids.Grid attribute) ExpressionContext (class in galaxy.util.expressions) ExpressionValidator (class in galaxy.tools.parameters.validation) expunge_all() (galaxy.managers.context.ProvidesAppContext method) ext (galaxy.model.DatasetInstance attribute) extend() (galaxy.model.custom_types.MutationList method) extend_data_with() (galaxy.tools.data.TabularToolDataTable method) extend_validation_errors() (galaxy.model.DatasetInstance method) ExtendedMetadata (class in galaxy.model) ExtendedMetadataIndex (class in galaxy.model) external (galaxy.webapps.tool_shed.model.User attribute) external_metadata_set_successfully() (galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper method) external_runjob() (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) external_service_grid (galaxy.webapps.galaxy.controllers.external_service.ExternalService attribute) external_services (galaxy.model.RequestType attribute) ExternalService (class in galaxy.model) (class in galaxy.webapps.galaxy.controllers.external_service) ExternalServiceAction (class in galaxy.external_services.actions) ExternalServiceActionJQueryGridResultHandler (class in galaxy.external_services.result_handlers.basic) ExternalServiceActionJSONResultHandler (class in galaxy.external_services.result_handlers.basic) ExternalServiceActionResultHandler (class in galaxy.external_services.result_handlers.basic) ExternalServiceActionsConditional (class in galaxy.external_services.service) ExternalServiceActionsGroup (class in galaxy.external_services.service) ExternalServiceActionsGroupWhen (class in galaxy.external_services.service) ExternalServiceActionURLRedirectResultHandler (class in galaxy.external_services.result_handlers.basic) ExternalServiceController (class in galaxy.webapps.galaxy.controllers.external_services) ExternalServiceGrid (class in galaxy.webapps.galaxy.controllers.external_service) ExternalServiceGrid.ExternalServiceTypeColumn (class in galaxy.webapps.galaxy.controllers.external_service) ExternalServiceGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.external_service) ExternalServiceParameter (class in galaxy.external_services.parameters) ExternalServiceResult (class in galaxy.external_services.actions) ExternalServiceTemplateAction (class in galaxy.external_services.actions) ExternalServiceTemplateParameter (class in galaxy.external_services.parameters) ExternalServiceType (class in galaxy.sample_tracking.external_service_types) ExternalServiceTypeNotFoundException ExternalServiceTypesCollection (class in galaxy.sample_tracking.external_service_types) ExternalServiceValueResult (class in galaxy.external_services.actions) ExternalServiceWebAction (class in galaxy.external_services.actions) ExternalServiceWebAPIAction (class in galaxy.external_services.actions) ExternalServiceWebAPIAction.ExternalServiceWebAPIActionRequest (class in galaxy.external_services.actions) ExternalServiceWebAPIActionResult (class in galaxy.external_services.actions) extra_files_path (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) extract_components_from_tuple() (in module tool_shed.util.shed_util_common) extract_value() (galaxy.tools.test.ParamContext method) extraction_error() (pkg_resources.ResourceManager method) extraction_path (pkg_resources.ResourceManager attribute) ExtractionError extras (pkg_resources.Distribution attribute) ez_setup (galaxy.eggs.scramble.ScrambleEgg attribute) ez_setup_url (galaxy.eggs.scramble.ScrambleEgg attribute)

F

fail() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.WorkflowInvocation method) (in module galaxy.tools.util.galaxyops) fail_job() (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.jobs.runners.lwr.LwrJobRunner method) FAILURE (galaxy.web.framework.openid_manager.OpenIDManager attribute) FakeTrans (class in galaxy.jobs.deferred) Fasta (class in galaxy.datatypes.sequence) fastaNamedReader (class in galaxy_utils.sequence.fasta) fastaReader (class in galaxy_utils.sequence.fasta) fastaSequence (class in galaxy_utils.sequence.fasta) fastaWriter (class in galaxy_utils.sequence.fasta) Fastq (class in galaxy.datatypes.sequence) fastqAggregator (class in galaxy_utils.sequence.fastq) fastqCombiner (class in galaxy_utils.sequence.fastq) FastqCSSanger (class in galaxy.datatypes.sequence) fastqCSSangerRead (class in galaxy_utils.sequence.fastq) fastqFakeFastaScoreReader (class in galaxy_utils.sequence.fastq) FastqIllumina (class in galaxy.datatypes.sequence) fastqIlluminaRead (class in galaxy_utils.sequence.fastq) fastqJoiner (class in galaxy_utils.sequence.fastq) fastqNamedReader (class in galaxy_utils.sequence.fastq) fastqReader (class in galaxy_utils.sequence.fastq) FastqSanger (class in galaxy.datatypes.sequence) fastqSangerRead (class in galaxy_utils.sequence.fastq) fastqSequencingRead (class in galaxy_utils.sequence.fastq) FastqSolexa (class in galaxy.datatypes.sequence) fastqSolexaRead (class in galaxy_utils.sequence.fastq) fastqSplitter (class in galaxy_utils.sequence.fastq) fastqVerboseErrorReader (class in galaxy_utils.sequence.fastq) fastqWriter (class in galaxy_utils.sequence.fastq) FeatureLocationIndex (class in galaxy.datatypes.tabular) fetch() (galaxy.eggs.Egg method) fetch_one() (galaxy.eggs.scramble.ScrambleEgg method) fetch_source() (galaxy.eggs.scramble.ScrambleEgg method) fetch_tool_versions() (in module tool_shed.galaxy_install.install_manager) field (in module galaxy.forms.forms) field_as_html() (galaxy.model.FormDefinition method) field_param_values_ok() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) fields() (galaxy.web.form_builder.AddressField static method) FieldStorage (class in galaxy.web.framework.base) file_ext (galaxy.datatypes.assembly.Amos attribute) (galaxy.datatypes.assembly.Velvet attribute) (galaxy.datatypes.binary.Ab1 attribute) (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.Bcf attribute) (galaxy.datatypes.binary.CompressedArchive attribute) (galaxy.datatypes.binary.GeminiSQLite attribute) (galaxy.datatypes.binary.GenericAsn1Binary attribute) (galaxy.datatypes.binary.H5 attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.binary.Scf attribute) (galaxy.datatypes.binary.Sff attribute) (galaxy.datatypes.binary.Sra attribute) (galaxy.datatypes.binary.TwoBit attribute) (galaxy.datatypes.binary.Xlsx attribute) (galaxy.datatypes.chrominfo.ChromInfo attribute) (galaxy.datatypes.coverage.LastzCoverage attribute) (galaxy.datatypes.data.GenericAsn1 attribute) (galaxy.datatypes.data.Newick attribute) (galaxy.datatypes.data.Nexus attribute) (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.genetics.Affybatch attribute) (galaxy.datatypes.genetics.Eigenstratgeno attribute) (galaxy.datatypes.genetics.Eigenstratpca attribute) (galaxy.datatypes.genetics.Eset attribute) (galaxy.datatypes.genetics.Fped attribute) (galaxy.datatypes.genetics.Fphe attribute) (galaxy.datatypes.genetics.GenomeGraphs attribute) (galaxy.datatypes.genetics.Lped attribute) (galaxy.datatypes.genetics.MAlist attribute) (galaxy.datatypes.genetics.Pbed attribute) (galaxy.datatypes.genetics.Phe attribute) (galaxy.datatypes.genetics.Pheno attribute) (galaxy.datatypes.genetics.Pphe attribute) (galaxy.datatypes.genetics.RexpBase attribute) (galaxy.datatypes.genetics.Rgenetics attribute) (galaxy.datatypes.genetics.SNPMatrix attribute) (galaxy.datatypes.genetics.Snptest attribute) (galaxy.datatypes.genetics.ldIndep attribute) (galaxy.datatypes.genetics.rgFeatureList attribute) (galaxy.datatypes.genetics.rgSampleList attribute) (galaxy.datatypes.genetics.rgTabList attribute) (galaxy.datatypes.images.Bmp attribute) (galaxy.datatypes.images.Eps attribute) (galaxy.datatypes.images.Gif attribute) (galaxy.datatypes.images.Gmaj attribute) (galaxy.datatypes.images.Html attribute) (galaxy.datatypes.images.Im attribute) (galaxy.datatypes.images.Jpg attribute) (galaxy.datatypes.images.Laj attribute) (galaxy.datatypes.images.Pbm attribute) (galaxy.datatypes.images.Pcd attribute) (galaxy.datatypes.images.Pcx attribute) (galaxy.datatypes.images.Pdf attribute) (galaxy.datatypes.images.Pgm attribute) (galaxy.datatypes.images.Png attribute) (galaxy.datatypes.images.Ppm attribute) (galaxy.datatypes.images.Psd attribute) (galaxy.datatypes.images.Rast attribute) (galaxy.datatypes.images.Rgb attribute) (galaxy.datatypes.images.Tiff attribute) (galaxy.datatypes.images.Xbm attribute) (galaxy.datatypes.images.Xpm attribute) (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.Bed12 attribute) (galaxy.datatypes.interval.Bed6 attribute) (galaxy.datatypes.interval.BedGraph attribute) (galaxy.datatypes.interval.BedStrict attribute) (galaxy.datatypes.interval.ChromatinInteractions attribute) (galaxy.datatypes.interval.CustomTrack attribute) (galaxy.datatypes.interval.ENCODEPeak attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Gff3 attribute) (galaxy.datatypes.interval.Gtf attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.ngsindex.BowtieBaseIndex attribute) (galaxy.datatypes.ngsindex.BowtieColorIndex attribute) (galaxy.datatypes.ngsindex.BowtieIndex attribute) (galaxy.datatypes.qualityscore.QualityScore attribute) (galaxy.datatypes.qualityscore.QualityScore454 attribute) (galaxy.datatypes.qualityscore.QualityScoreIllumina attribute) (galaxy.datatypes.qualityscore.QualityScoreSOLiD attribute) (galaxy.datatypes.qualityscore.QualityScoreSolexa attribute) (galaxy.datatypes.sequence.Axt attribute) (galaxy.datatypes.sequence.Fasta attribute) (galaxy.datatypes.sequence.Fastq attribute) (galaxy.datatypes.sequence.FastqCSSanger attribute) (galaxy.datatypes.sequence.FastqIllumina attribute) (galaxy.datatypes.sequence.FastqSanger attribute) (galaxy.datatypes.sequence.FastqSolexa attribute) (galaxy.datatypes.sequence.Lav attribute) (galaxy.datatypes.sequence.Maf attribute) (galaxy.datatypes.sequence.MafCustomTrack attribute) (galaxy.datatypes.sequence.RNADotPlotMatrix attribute) (galaxy.datatypes.sequence.SequenceSplitLocations attribute) (galaxy.datatypes.sequence.csFasta attribute) (galaxy.datatypes.tabular.Eland attribute) (galaxy.datatypes.tabular.ElandMulti attribute) (galaxy.datatypes.tabular.FeatureLocationIndex attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.tabular.Vcf attribute) (galaxy.datatypes.tracks.GeneTrack attribute) (galaxy.datatypes.xml.CisML attribute) (galaxy.datatypes.xml.GenericXml attribute) (galaxy.datatypes.xml.MEMEXml attribute) (galaxy.datatypes.xml.Owl attribute) (galaxy.datatypes.xml.Phyloxml attribute) file_iter() (in module galaxy.util) file_name (galaxy.datatypes.metadata.MetadataTempFile attribute) (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.MetadataFile attribute) file_path (galaxy.model.Dataset attribute) file_reader() (in module galaxy.util) file_ready() (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) file_states (galaxy.webapps.tool_shed.model.Repository attribute) FileField (class in galaxy.web.form_builder) FileMetadata (class in pkg_resources) FileParameter (class in galaxy.datatypes.metadata) FileToolParameter (class in galaxy.tools.parameters.basic) fill_in_new_state() (galaxy.tools.Tool method) fill_region_alignment() (in module galaxy.tools.util.maf_utilities) fill_template() (in module galaxy.util.template) Filter (class in galaxy.tools.parameters.dynamic_options) filter() (galaxy.web.framework.helpers.grids.CommunityTagsColumn method) (galaxy.web.framework.helpers.grids.DeletedColumn method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.framework.helpers.grids.MulticolFilterColumn method) (galaxy.web.framework.helpers.grids.SharingStatusColumn method) (galaxy.web.framework.helpers.grids.StateColumn method) (galaxy.web.framework.helpers.grids.TextColumn method) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid.StateColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.EmailColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.SpecifiedDateColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.StateColumn method) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid.EmailColumn method) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid.SpecifiedDateColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.EmailColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.SpecifiedDateColumn method) (tool_shed.grids.admin_grids.UserGrid.EmailColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.EmailColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.RepositoryCategoryColumn method) (tool_shed.grids.repository_grids.ValidRepositoryGrid.RepositoryCategoryColumn method) filter_by_dataset() (galaxy.datatypes.display_applications.application.DisplayApplication method) (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) filter_by_latest_downloadable_changeset_revision_that_has_failing_tool_tests() (in module tool_shed.grids.util) filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components() (in module tool_shed.grids.util) filter_by_latest_downloadable_changeset_revision_that_has_no_failing_tool_tests() (in module tool_shed.grids.util) filter_by_latest_downloadable_changeset_revision_that_has_test_install_errors() (in module tool_shed.grids.util) filter_by_latest_downloadable_changeset_revision_with_skip_tests_checked() (in module tool_shed.grids.util) filter_by_latest_metadata_changeset_revision_that_has_invalid_tools() (in module tool_shed.grids.util) filter_file_fields() (galaxy.tools.data.TabularToolDataTable method) filter_options() (galaxy.tools.parameters.dynamic_options.AdditionalValueFilter method) (galaxy.tools.parameters.dynamic_options.AttributeValueSplitterFilter method) (galaxy.tools.parameters.dynamic_options.DataMetaFilter method) (galaxy.tools.parameters.dynamic_options.Filter method) (galaxy.tools.parameters.dynamic_options.MultipleSplitterFilter method) (galaxy.tools.parameters.dynamic_options.ParamValueFilter method) (galaxy.tools.parameters.dynamic_options.RemoveValueFilter method) (galaxy.tools.parameters.dynamic_options.SortByColumnFilter method) (galaxy.tools.parameters.dynamic_options.StaticValueFilter method) (galaxy.tools.parameters.dynamic_options.UniqueValueFilter method) (galaxy.tools.parameters.output.BooleanFilter method) (galaxy.tools.parameters.output.ColumnReplaceFilter method) (galaxy.tools.parameters.output.ColumnStripFilter method) (galaxy.tools.parameters.output.InsertColumnToolOutputActionOptionFilter method) (galaxy.tools.parameters.output.MetadataValueFilter method) (galaxy.tools.parameters.output.MultipleSplitterFilter method) (galaxy.tools.parameters.output.ParamValueToolOutputActionOptionFilter method) (galaxy.tools.parameters.output.StringFunctionFilter method) (galaxy.tools.parameters.output.ToolOutputActionOptionFilter method) filter_output() (in module galaxy.tools.actions) filter_type (in module galaxy.tools.parameters.output) filter_value() (galaxy.tools.parameters.basic.ToolParameter method) final_sample_state (galaxy.model.RequestType attribute) finalize_config() (galaxy.web.framework.base.WebApplication method) find() (pkg_resources.WorkingSet method) find_class() (galaxy.util.aliaspickler.AliasUnpickler method) find_conversion_destination() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) find_conversion_destination_for_dataset_by_extensions() (galaxy.datatypes.registry.Registry method) find_dep() (galaxy.tools.deps.DependencyManager method) (galaxy.tools.deps.NullDependencyManager method) find_distributions() (in module pkg_resources) find_fieldstorage() (galaxy.tools.Tool method) find_implicit_input_collection() (galaxy.model.HistoryDatasetCollectionAssociation method) find_output_def() (galaxy.tools.Tool method)

find_plugins() (pkg_resources.WorkingSet method) find_samples() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) find_samples_index() (galaxy.webapps.galaxy.controllers.requests.Requests method) find_tools() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) find_tools_in_tool_shed() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) find_workflows() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) find_workflows_in_tool_shed() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) finish() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) finish_job() (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.lwr.LwrJobRunner method) finished (galaxy.model.Job attribute) first_dataset_instance() (galaxy.model.DatasetCollectionElement method) fitness_and_quality_parsed() (in module mimeparse) fixup_namespace_packages() (in module pkg_resources) flatten() (galaxy.util.Params method) (in module galaxy.web.framework.base) FloatToolParameter (class in galaxy.tools.parameters.basic) flush() (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.TempFileHandler method) fn_filter_parsers (galaxy.managers.base.ModelFilterParser attribute) folder_info() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) folder_is_public() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) folder_is_unrestricted() (galaxy.security.GalaxyRBACAgent method) folder_permissions() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) FolderContentsController (class in galaxy.webapps.galaxy.api.folder_contents) FolderManager (class in galaxy.managers.folders) FoldersController (class in galaxy.webapps.galaxy.api.folders) for_direct_import() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) for_state() (galaxy.tools.test.ParamContext method) (galaxy.tools.test.RootParamContext method) force_bed_field_count() (in module galaxy.datatypes.converters.interval_to_bedstrict_converter) force_symlink() (in module galaxy.util) foreign_key_name (galaxy.managers.base.ModelManager attribute) (galaxy.managers.hdas.HDAManager attribute) (galaxy.managers.histories.HistoryManager attribute) (galaxy.managers.roles.RoleManager attribute) foreignKey() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) format (galaxy.web.framework.middleware.translogger.TransLogger attribute) (galaxy_utils.sequence.fastq.fastqCSSangerRead attribute) (galaxy_utils.sequence.fastq.fastqIlluminaRead attribute) (galaxy_utils.sequence.fastq.fastqSangerRead attribute) (galaxy_utils.sequence.fastq.fastqSequencingRead attribute) (galaxy_utils.sequence.fastq.fastqSolexaRead attribute) (in module galaxy_utils.sequence.fastq) (in module galaxy_utils.sequence.vcf) format_bool() (in module galaxy.webapps.galaxy.controllers.page) format_traceback() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) formats (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter attribute) FormatToolOutputAction (class in galaxy.tools.parameters.output) FormDefinition (class in galaxy.model) FormDefinitionAddressFieldFactory (class in galaxy.forms.forms) FormDefinitionAPIController (class in galaxy.webapps.galaxy.api.forms) FormDefinitionCurrent (class in galaxy.model) FormDefinitionFactory (class in galaxy.forms.forms) FormDefinitionFieldFactory (class in galaxy.forms.forms) FormDefinitionHistoryFieldFactory (class in galaxy.forms.forms) FormDefinitionPasswordFieldFactory (class in galaxy.forms.forms) FormDefinitionSelectFieldFactory (class in galaxy.forms.forms) FormDefinitionTextFieldFactory (class in galaxy.forms.forms) FormDefinitionWorkflowFieldFactory (class in galaxy.forms.forms) FormDefinitionWorkflowMappingFieldFactory (class in galaxy.forms.forms) Forms (class in galaxy.webapps.galaxy.controllers.forms) forms_grid (galaxy.webapps.galaxy.controllers.forms.Forms attribute) FormsGrid (class in galaxy.webapps.galaxy.controllers.forms) FormsGrid.DescriptionColumn (class in galaxy.webapps.galaxy.controllers.forms) FormsGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.forms) FormsGrid.TypeColumn (class in galaxy.webapps.galaxy.controllers.forms) FormValues (class in galaxy.model) Fped (class in galaxy.datatypes.genetics) Fphe (class in galaxy.datatypes.genetics) from_dict() (galaxy.visualization.genomes.GenomeRegion static method) (galaxy.workflow.modules.SimpleWorkflowModule class method) (galaxy.workflow.modules.ToolModule class method) (galaxy.workflow.modules.WorkflowModule class method) (galaxy.workflow.modules.WorkflowModuleFactory method) (tool_shed.util.workflow_util.RepoToolModule class method) (tool_shed.util.workflow_util.RepoWorkflowModuleFactory method) from_elem() (galaxy.datatypes.display_applications.application.DisplayApplication class method) (galaxy.datatypes.display_applications.application.DisplayApplicationLink class method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter class method) (galaxy.external_services.actions.ExternalServiceAction class method) (galaxy.external_services.parameters.ExternalServiceParameter class method) (galaxy.external_services.result_handlers.basic.ExternalServiceActionResultHandler class method) (galaxy.external_services.result_handlers.basic.ExternalServiceActionURLRedirectResultHandler class method) (galaxy.external_services.service.BooleanExternalServiceActionsGroupWhen class method) (galaxy.external_services.service.ExternalServiceActionsGroup class method) (galaxy.external_services.service.ExternalServiceActionsGroupWhen class method) (galaxy.external_services.service.ItemIsInstanceExternalServiceActionsGroupWhen class method) (galaxy.external_services.service.ValueExternalServiceActionsGroupWhen class method) (galaxy.forms.forms.FormDefinitionAddressFieldFactory method) (galaxy.forms.forms.FormDefinitionFactory method) (galaxy.forms.forms.FormDefinitionFieldFactory method) (galaxy.forms.forms.FormDefinitionHistoryFieldFactory method) (galaxy.forms.forms.FormDefinitionPasswordFieldFactory method) (galaxy.forms.forms.FormDefinitionSelectFieldFactory method) (galaxy.forms.forms.FormDefinitionTextFieldFactory method) (galaxy.forms.forms.FormDefinitionWorkflowFieldFactory method) (galaxy.forms.forms.FormDefinitionWorkflowMappingFieldFactory method) (galaxy.openid.providers.OpenIDProvider class method) (galaxy.openid.providers.OpenIDProviders class method) (galaxy.sample_tracking.request_types.RequestTypeFactory method) (galaxy.sample_tracking.sample.SampleStateFactory method) (galaxy.tools.data.ToolDataTable class method) (galaxy.tools.parameters.output.ToolOutputAction class method) (galaxy.tools.parameters.output.ToolOutputActionConditionalWhen class method) (galaxy.tools.parameters.output.ToolOutputActionOption class method) (galaxy.tools.parameters.output.ToolOutputActionOptionFilter class method) from_element() (galaxy.tools.parameters.dynamic_options.Filter class method) (galaxy.tools.parameters.input_translation.ToolInputTranslator class method) (galaxy.tools.parameters.sanitize.ToolParameterSanitizer class method) (galaxy.tools.parameters.validation.DatasetOkValidator class method) (galaxy.tools.parameters.validation.EmptyTextfieldValidator class method) (galaxy.tools.parameters.validation.ExpressionValidator class method) (galaxy.tools.parameters.validation.InRangeValidator class method) (galaxy.tools.parameters.validation.LengthValidator class method) (galaxy.tools.parameters.validation.MetadataInDataTableColumnValidator class method) (galaxy.tools.parameters.validation.MetadataInFileColumnValidator class method) (galaxy.tools.parameters.validation.MetadataValidator class method) (galaxy.tools.parameters.validation.NoOptionsValidator class method) (galaxy.tools.parameters.validation.RegexValidator class method) (galaxy.tools.parameters.validation.UnspecifiedBuildValidator class method) (galaxy.tools.parameters.validation.Validator class method) from_external_value() (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) from_file() (galaxy.datatypes.display_applications.application.DisplayApplication class method) (galaxy.openid.providers.OpenIDProvider class method) (galaxy.openid.providers.OpenIDProviders class method) from_filename() (pkg_resources.Distribution class method) from_html() (galaxy.tools.parameters.basic.BaseURLToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter method) (galaxy.tools.parameters.basic.IntegerToolParameter method) (galaxy.tools.parameters.basic.LibraryDatasetToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) from_JSON() (galaxy.datatypes.metadata.MetadataTempFile class method) from_json() (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) from_JSON_dict() (galaxy.datatypes.metadata.MetadataCollection method) from_location() (pkg_resources.Distribution class method) from_str() (galaxy.visualization.genomes.GenomeRegion static method) from_workflow_step() (galaxy.workflow.modules.SimpleWorkflowModule class method) (galaxy.workflow.modules.ToolModule class method) (galaxy.workflow.modules.WorkflowModule class method) (galaxy.workflow.modules.WorkflowModuleFactory method) (tool_shed.util.workflow_util.RepoToolModule class method) (tool_shed.util.workflow_util.RepoWorkflowModuleFactory method) FromDataTableOutputActionOption (class in galaxy.tools.parameters.output) FromFileToolOutputActionOption (class in galaxy.tools.parameters.output) FromParamToolOutputActionOption (class in galaxy.tools.parameters.output) FtpDataTransferFactory (class in galaxy.sample_tracking.data_transfer) FTPFileField (class in galaxy.web.form_builder) FTPFileToolParameter (class in galaxy.tools.parameters.basic) full_delete() (galaxy.model.Dataset method) func_std_string() (in module galaxy.web.framework.middleware.profile)

G

galaxy (module) galaxy.actions.admin (module) galaxy.config (module) galaxy.datatypes.assembly (module) galaxy.datatypes.binary (module) galaxy.datatypes.checkers (module) galaxy.datatypes.chrominfo (module) galaxy.datatypes.converters.bed_to_gff_converter (module) galaxy.datatypes.converters.bgzip (module) galaxy.datatypes.converters.fasta_to_len (module) galaxy.datatypes.converters.fasta_to_tabular_converter (module) galaxy.datatypes.converters.fastq_to_fqtoc (module) galaxy.datatypes.converters.fastqsolexa_to_fasta_converter (module) galaxy.datatypes.converters.fastqsolexa_to_qual_converter (module) galaxy.datatypes.converters.gff_to_bed_converter (module) galaxy.datatypes.converters.gff_to_interval_index_converter (module) galaxy.datatypes.converters.interval_to_bed_converter (module) galaxy.datatypes.converters.interval_to_bedstrict_converter (module) galaxy.datatypes.converters.interval_to_coverage (module) galaxy.datatypes.converters.interval_to_fli (module) galaxy.datatypes.converters.interval_to_interval_index_converter (module) galaxy.datatypes.converters.interval_to_tabix_converter (module) galaxy.datatypes.converters.lped_to_fped_converter (module) galaxy.datatypes.converters.lped_to_pbed_converter (module) galaxy.datatypes.converters.maf_to_fasta_converter (module) galaxy.datatypes.converters.maf_to_interval_converter (module) galaxy.datatypes.converters.pbed_ldreduced_converter (module) galaxy.datatypes.converters.pbed_to_lped_converter (module) galaxy.datatypes.converters.picard_interval_list_to_bed6_converter (module) galaxy.datatypes.converters.sam_to_bam (module) galaxy.datatypes.converters.vcf_to_interval_index_converter (module) galaxy.datatypes.converters.vcf_to_vcf_bgzip (module) galaxy.datatypes.converters.wiggle_to_array_tree_converter (module) galaxy.datatypes.converters.wiggle_to_simple_converter (module) galaxy.datatypes.coverage (module) galaxy.datatypes.data (module) galaxy.datatypes.display_applications.application (module) galaxy.datatypes.display_applications.parameters (module) galaxy.datatypes.display_applications.util (module) galaxy.datatypes.genetics (module) galaxy.datatypes.images (module) galaxy.datatypes.interval (module) galaxy.datatypes.metadata (module) galaxy.datatypes.ngsindex (module) galaxy.datatypes.qualityscore (module) galaxy.datatypes.registry (module) galaxy.datatypes.sequence (module) galaxy.datatypes.sniff (module) galaxy.datatypes.tabular (module) galaxy.datatypes.tracks (module) galaxy.datatypes.util (module) galaxy.datatypes.util.gff_util (module) galaxy.datatypes.util.image_util (module) galaxy.datatypes.xml (module) galaxy.eggs (module) galaxy.eggs.dist (module) galaxy.eggs.scramble (module) galaxy.exceptions (module) galaxy.external_services.actions (module) galaxy.external_services.parameters (module) galaxy.external_services.result_handlers.basic (module) galaxy.external_services.service (module) galaxy.forms.forms (module) galaxy.jobs (module) galaxy.jobs.actions (module) galaxy.jobs.actions.post (module) galaxy.jobs.deferred (module) galaxy.jobs.deferred.data_transfer (module) galaxy.jobs.deferred.manual_data_transfer (module) galaxy.jobs.deferred.pacific_biosciences_smrt_portal (module) galaxy.jobs.handler (module) galaxy.jobs.manager (module) galaxy.jobs.mapper (module) galaxy.jobs.runners (module) galaxy.jobs.runners.cli (module) galaxy.jobs.runners.condor (module) galaxy.jobs.runners.drmaa (module) galaxy.jobs.runners.local (module) galaxy.jobs.runners.lwr (module) galaxy.jobs.runners.tasks (module) galaxy.jobs.splitters.basic (module) galaxy.jobs.splitters.multi (module) galaxy.jobs.transfer_manager (module) galaxy.managers (module) galaxy.managers.api_keys (module) galaxy.managers.base (module) galaxy.managers.citations (module) galaxy.managers.collections (module) galaxy.managers.collections_util (module) galaxy.managers.context (module) galaxy.managers.folders (module) galaxy.managers.hdas (module) galaxy.managers.histories (module) galaxy.managers.lddas (module) galaxy.managers.libraries (module) galaxy.managers.roles (module) galaxy.managers.tags (module) galaxy.managers.workflows (module) galaxy.model (module) galaxy.model.custom_types (module) galaxy.model.item_attrs (module) galaxy.model.mapping (module) galaxy.model.migrate.check (module) galaxy.model.orm (module) galaxy.model.orm.logging_connection_proxy (module) galaxy.objectstore (module) galaxy.objectstore.s3_multipart_upload (module) galaxy.openid (module) galaxy.openid.providers (module) galaxy.quota (module) galaxy.sample_tracking.data_transfer (module) galaxy.sample_tracking.external_service_types (module) galaxy.sample_tracking.request_types (module) galaxy.sample_tracking.sample (module) galaxy.security (module) galaxy.security.validate_user_input (module) galaxy.tags (module) galaxy.tags.tag_handler (module) galaxy.tools (module) galaxy.tools.actions (module) galaxy.tools.actions.history_imp_exp (module) galaxy.tools.actions.metadata (module) galaxy.tools.actions.upload (module) galaxy.tools.actions.upload_common (module) galaxy.tools.data (module) galaxy.tools.deps (module) galaxy.tools.exception_handling (module) galaxy.tools.imp_exp (module) galaxy.tools.imp_exp.export_history (module) galaxy.tools.imp_exp.unpack_tar_gz_archive (module) galaxy.tools.parameters (module) galaxy.tools.parameters.basic (module) galaxy.tools.parameters.dynamic_options (module) galaxy.tools.parameters.grouping (module) galaxy.tools.parameters.input_translation (module) galaxy.tools.parameters.output (module) galaxy.tools.parameters.sanitize (module) galaxy.tools.parameters.validation (module) galaxy.tools.search (module) galaxy.tools.test (module) galaxy.tools.util (module) galaxy.tools.util.galaxyops (module) galaxy.tools.util.maf_utilities (module) galaxy.util (module) galaxy.util.aliaspickler (module) galaxy.util.backports (module) galaxy.util.backports.importlib (module) galaxy.util.bunch (module) galaxy.util.debugging (module) galaxy.util.expressions (module) galaxy.util.hash_util (module) galaxy.util.heartbeat (module) galaxy.util.inflection (module) galaxy.util.json (module) galaxy.util.lrucache (module) galaxy.util.none_like (module) galaxy.util.odict (module) galaxy.util.sanitize_html (module) galaxy.util.streamball (module) galaxy.util.template (module) galaxy.util.topsort (module) galaxy.visualization (module) galaxy.visualization.data_providers (module) galaxy.visualization.data_providers.basic (module) galaxy.visualization.data_providers.phyloviz (module) galaxy.visualization.data_providers.phyloviz.baseparser (module) galaxy.visualization.data_providers.phyloviz.newickparser (module) galaxy.visualization.data_providers.phyloviz.nexusparser (module) galaxy.visualization.data_providers.phyloviz.phyloxmlparser (module) galaxy.visualization.genome (module) galaxy.visualization.genomes (module) galaxy.visualization.tracks (module) galaxy.web (module) galaxy.web.base.controller (module) galaxy.web.base.controllers.admin (module) galaxy.web.form_builder (module) galaxy.web.framework (module) galaxy.web.framework.base (module) galaxy.web.framework.helpers (module) galaxy.web.framework.helpers.grids (module) galaxy.web.framework.middleware (module) galaxy.web.framework.middleware.profile (module) galaxy.web.framework.middleware.remoteuser (module) galaxy.web.framework.middleware.static (module) galaxy.web.framework.middleware.translogger (module) galaxy.web.framework.middleware.xforwardedhost (module) galaxy.web.framework.openid_manager (module) galaxy.web.params (module) galaxy.web.security (module) galaxy.webapps (module) galaxy.webapps.galaxy.api.annotations (module) galaxy.webapps.galaxy.api.authenticate (module) galaxy.webapps.galaxy.api.configuration (module) galaxy.webapps.galaxy.api.dataset_collections (module) galaxy.webapps.galaxy.api.datatypes (module) galaxy.webapps.galaxy.api.extended_metadata (module) galaxy.webapps.galaxy.api.folder_contents (module) galaxy.webapps.galaxy.api.folders (module) galaxy.webapps.galaxy.api.forms (module) galaxy.webapps.galaxy.api.genomes (module) galaxy.webapps.galaxy.api.group_roles (module) galaxy.webapps.galaxy.api.group_users (module) galaxy.webapps.galaxy.api.groups (module) galaxy.webapps.galaxy.api.histories (module) galaxy.webapps.galaxy.api.history_contents (module) galaxy.webapps.galaxy.api.item_tags (module) galaxy.webapps.galaxy.api.job_files (module) galaxy.webapps.galaxy.api.jobs (module) galaxy.webapps.galaxy.api.lda_datasets (module) galaxy.webapps.galaxy.api.libraries (module) galaxy.webapps.galaxy.api.library_contents (module) galaxy.webapps.galaxy.api.metrics (module) galaxy.webapps.galaxy.api.page_revisions (module) galaxy.webapps.galaxy.api.pages (module) galaxy.webapps.galaxy.api.provenance (module) galaxy.webapps.galaxy.api.quotas (module) galaxy.webapps.galaxy.api.request_types (module) galaxy.webapps.galaxy.api.requests (module) galaxy.webapps.galaxy.api.roles (module) galaxy.webapps.galaxy.api.samples (module) galaxy.webapps.galaxy.api.search (module) galaxy.webapps.galaxy.api.tool_data (module) galaxy.webapps.galaxy.api.tool_shed_repositories (module) galaxy.webapps.galaxy.api.users (module) galaxy.webapps.galaxy.api.visualizations (module) galaxy.webapps.galaxy.api.workflows (module) galaxy.webapps.galaxy.controllers (module) galaxy.webapps.galaxy.controllers.admin (module) galaxy.webapps.galaxy.controllers.admin_toolshed (module) galaxy.webapps.galaxy.controllers.async (module) galaxy.webapps.galaxy.controllers.dataset (module) galaxy.webapps.galaxy.controllers.error (module) galaxy.webapps.galaxy.controllers.external_service (module) galaxy.webapps.galaxy.controllers.external_services (module) galaxy.webapps.galaxy.controllers.forms (module) galaxy.webapps.galaxy.controllers.history (module) galaxy.webapps.galaxy.controllers.library (module) galaxy.webapps.galaxy.controllers.library_admin (module) galaxy.webapps.galaxy.controllers.library_common (module) galaxy.webapps.galaxy.controllers.mobile (module) galaxy.webapps.galaxy.controllers.page (module) galaxy.webapps.galaxy.controllers.request_type (module) galaxy.webapps.galaxy.controllers.requests (module) galaxy.webapps.galaxy.controllers.requests_admin (module) galaxy.webapps.galaxy.controllers.requests_common (module) galaxy.webapps.galaxy.controllers.root (module) galaxy.webapps.galaxy.controllers.tag (module) galaxy.webapps.galaxy.controllers.tool_runner (module) galaxy.webapps.galaxy.controllers.ucsc_proxy (module) galaxy.webapps.galaxy.controllers.user (module) galaxy.webapps.galaxy.controllers.workflow (module) galaxy.webapps.reports (module) galaxy.webapps.reports.app (module) galaxy.webapps.reports.buildapp (module) galaxy.webapps.reports.config (module) galaxy.webapps.reports.controllers (module) galaxy.webapps.reports.controllers.jobs (module) galaxy.webapps.reports.controllers.root (module) galaxy.webapps.reports.controllers.sample_tracking (module) galaxy.webapps.reports.controllers.system (module) galaxy.webapps.reports.controllers.users (module) galaxy.webapps.reports.controllers.workflows (module) galaxy.webapps.tool_shed (module) galaxy.webapps.tool_shed.api.repositories (module) galaxy.webapps.tool_shed.api.repository_revisions (module) galaxy.webapps.tool_shed.app (module) galaxy.webapps.tool_shed.buildapp (module) galaxy.webapps.tool_shed.config (module) galaxy.webapps.tool_shed.controllers (module) galaxy.webapps.tool_shed.controllers.admin (module) galaxy.webapps.tool_shed.controllers.hg (module) galaxy.webapps.tool_shed.controllers.repository (module) galaxy.webapps.tool_shed.controllers.repository_review (module) galaxy.webapps.tool_shed.controllers.upload (module) galaxy.webapps.tool_shed.controllers.user (module) galaxy.webapps.tool_shed.framework (module) galaxy.webapps.tool_shed.framework.middleware (module) galaxy.webapps.tool_shed.framework.middleware.hg (module) galaxy.webapps.tool_shed.framework.middleware.remoteuser (module) galaxy.webapps.tool_shed.model (module) galaxy.webapps.tool_shed.model.mapping (module) galaxy.webapps.tool_shed.model.migrate.check (module) galaxy.webapps.tool_shed.security (module) galaxy.webapps.tool_shed.util.hgweb_config (module) galaxy.webapps.tool_shed.util.shed_statistics (module) galaxy.workflow.modules (module) galaxy_directory() (in module galaxy.util) galaxy_lib_dir (galaxy.jobs.JobWrapper attribute) galaxy_sessions (galaxy.webapps.tool_shed.model.User attribute) galaxy_system_pwent (galaxy.jobs.JobWrapper attribute) galaxy_utils.sequence.fasta (module) galaxy_utils.sequence.fastq (module) galaxy_utils.sequence.sequence (module) galaxy_utils.sequence.transform (module) galaxy_utils.sequence.vcf (module) GalaxyConfig (class in galaxy.eggs) GalaxyRBACAgent (class in galaxy.security) GalaxySession (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) GalaxySessionToHistoryAssociation (class in galaxy.model) GalaxyTagManager (class in galaxy.managers.tags) gbrowse_links() (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Wiggle method) GeminiSQLite (class in galaxy.datatypes.binary) gen_image() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) generate_auto_primary_file() (galaxy.datatypes.data.Data method) generate_clone_url_for_installed_repository() (in module tool_shed.util.common_util) generate_clone_url_for_repository_in_tool_shed() (in module tool_shed.util.common_util) generate_clone_url_from_repo_info_tup() (in module tool_shed.util.common_util) generate_deprecated_repository_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_error() (galaxy.webapps.galaxy.controllers.root.RootController method) generate_includes_workflows_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_json_error() (galaxy.webapps.galaxy.controllers.root.RootController method) generate_latest_revision_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_message_for_invalid_tools() (in module tool_shed.util.tool_util) generate_primary_file() (galaxy.datatypes.assembly.Velvet method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.Rgenetics method) (galaxy.datatypes.ngsindex.BowtieIndex method) generate_revision_updates_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_revision_upgrades_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_sharable_link_for_repository_in_tool_shed() (in module tool_shed.util.shed_util_common) generate_statistics() (galaxy.webapps.tool_shed.util.shed_statistics.ShedCounter method) generate_tool_guid() (in module tool_shed.util.shed_util_common) generate_tool_shed_repository_install_dir() (in module tool_shed.util.shed_util_common) generate_unknown_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_workflow_image() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (in module tool_shed.util.workflow_util) generateJsonableDict() (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method) GenericAsn1 (class in galaxy.datatypes.data) GenericAsn1Binary (class in galaxy.datatypes.binary) GenericXml (class in galaxy.datatypes.xml) GeneTrack (class in galaxy.datatypes.tracks) Genome (class in galaxy.visualization.genomes) genome_build() (galaxy.managers.base.ModelValidator method) GenomeBuildParameter (class in galaxy.tools.parameters.basic) GenomeGraphs (class in galaxy.datatypes.genetics) GenomeIndexTool (class in galaxy.tools) GenomeIndexToolData (class in galaxy.model) GenomeRegion (class in galaxy.visualization.genomes) Genomes (class in galaxy.visualization.genomes) GenomesController (class in galaxy.webapps.galaxy.api.genomes) genomic_region_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.Pileup method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.Vcf method) genomic_region_dict_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.Pileup method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.Vcf method) GenomicRegionAlignment (class in galaxy.tools.util.maf_utilities) get() (galaxy.config.Configuration method) (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.datatypes.metadata.MetadataElementSpec method) (galaxy.managers.folders.FolderManager method) (galaxy.managers.lddas.LDDAManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.roles.RoleManager method) (galaxy.openid.providers.OpenIDProviders method) (galaxy.tools.data.ToolDataTableManager method) (galaxy.util.Params method) (galaxy.util.bunch.Bunch method) (galaxy.webapps.reports.config.Configuration method) (galaxy.webapps.tool_shed.config.Configuration method) (galaxy_utils.sequence.fasta.fastaNamedReader method) (galaxy_utils.sequence.fastq.fastqFakeFastaScoreReader method) (galaxy_utils.sequence.fastq.fastqNamedReader method) get_absolute_path_to_file_in_repository() (in module tool_shed.util.shed_util_common) get_accepted_filters() (galaxy.web.framework.helpers.grids.DeletedColumn method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.framework.helpers.grids.SharingStatusColumn method) (galaxy.web.framework.helpers.grids.StateColumn method) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid.StatusColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.DeletedColumn method) get_access_roles() (galaxy.managers.libraries.LibraryManager method) (galaxy.model.Dataset method) (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.Library method) (galaxy.model.LibraryDatasetDatasetAssociation method) get_accessible_libraries() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_accessible_request_types() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_action() (galaxy.security.RBACAgent method) (galaxy.webapps.tool_shed.security.RBACAgent method) get_action_access_link() (galaxy.external_services.actions.ExternalServiceAction method) (galaxy.external_services.actions.ExternalServiceWebAction method) (galaxy.external_services.actions.PopulatedExternalServiceAction method) get_action_by_name() (galaxy.external_services.service.PopulatedExternalService method) get_actions() (galaxy.security.RBACAgent method) (galaxy.webapps.tool_shed.security.RBACAgent method) get_actions_for_items() (galaxy.security.GalaxyRBACAgent method) get_activation_token() (galaxy.webapps.galaxy.controllers.user.User method) get_active_folders() (galaxy.model.Library method) get_add_list() (galaxy.jobs.actions.post.ActionBox class method) get_add_roles() (galaxy.managers.libraries.LibraryManager method) get_all_forms() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) get_all_forms_by_type() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) get_all_roles() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_amount() (galaxy.model.Quota method) get_annotation_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) get_api_key() (galaxy.webapps.galaxy.api.authenticate.AuthenticationController method) get_ascii_quality_scores() (galaxy_utils.sequence.fastq.fastqSequencingRead method) get_ascii_quality_scores_len() (galaxy_utils.sequence.fastq.fastqSequencingRead method) get_ascii_range() (galaxy_utils.sequence.fastq.fastqAggregator method) get_attributes_from_fasta_header() (in module galaxy.tools.util.maf_utilities) get_available_tracks() (galaxy.datatypes.registry.Registry method) get_ave_item_rating_data() (galaxy.model.item_attrs.UsesItemRatings method) get_base_counts_for_column() (galaxy_utils.sequence.fastq.fastqAggregator method) get_base_dir() (galaxy.tools.data.TabularToolDataField method) get_base_path() (galaxy.tools.data.TabularToolDataField method) get_bibtex() (galaxy.managers.citations.DoiCache method) get_bool() (galaxy.config.Configuration method) (galaxy.webapps.tool_shed.config.Configuration method) get_build() (galaxy.visualization.genomes.Genomes method) get_cache_path() (pkg_resources.ResourceManager method) get_categories() (in module tool_shed.util.shed_util_common) get_category() (in module tool_shed.util.shed_util_common) get_category_by_name() (in module tool_shed.util.shed_util_common) get_changeset_revision_and_ctx_rev() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_changesets_for_setting_metadata() (galaxy.webapps.tool_shed.model.Repository method) get_charset_from_http_headers() (in module galaxy.util) get_check_interval() (galaxy.model.DeferredJob method) get_child_by_designation() (galaxy.model.DatasetInstance method) get_chopped_blocks_for_region() (in module galaxy.tools.util.maf_utilities) get_chopped_blocks_with_index_offset_for_region() (in module galaxy.tools.util.maf_utilities) get_chunk() (galaxy.datatypes.tabular.Tabular method) get_class() (galaxy.web.base.controller.BaseController method) (in module galaxy.managers.base) get_class_by_format() (galaxy_utils.sequence.fastq.fastqSequencingRead class method) (galaxy_utils.sequence.vcf.VariantCall class method) get_cli_plugins() (galaxy.jobs.runners.cli.ShellJobRunner method) get_client() (galaxy.jobs.runners.lwr.LwrJobRunner method) get_client_from_state() (galaxy.jobs.runners.lwr.LwrJobRunner method) get_client_from_wrapper() (galaxy.jobs.runners.lwr.LwrJobRunner method) get_column_list() (galaxy.tools.parameters.basic.ColumnListParameter method) get_column_name_list() (galaxy.tools.data.TabularToolDataTable method) get_command_line() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) get_community_tags() (galaxy.managers.tags.TagManager method) get_component() (in module tool_shed.util.review_util) get_component_associations() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_component_by_name() (in module tool_shed.util.review_util) get_component_review() (in module tool_shed.util.review_util) get_component_review_by_repository_review_id_component_id() (in module tool_shed.util.review_util) get_components() (in module tool_shed.util.review_util) get_components_by_src() (in module galaxy.tools.util.maf_utilities) get_components_by_src_start() (in module galaxy.tools.util.maf_utilities) get_composite_dataset_name() (galaxy.tools.parameters.grouping.UploadDataset method) get_composite_extensions() (galaxy.datatypes.registry.Registry method) get_composite_files() (galaxy.datatypes.data.Data method) get_comptypes() (in module galaxy.webapps.galaxy.controllers.library_common) get_config_dict() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method) get_config_form() (galaxy.jobs.actions.post.ChangeDatatypeAction class method) (galaxy.jobs.actions.post.ColumnSetAction class method) (galaxy.jobs.actions.post.DefaultJobAction class method) (galaxy.jobs.actions.post.DeleteDatasetAction class method) (galaxy.jobs.actions.post.DeleteIntermediatesAction class method) (galaxy.jobs.actions.post.EmailAction class method) (galaxy.jobs.actions.post.HideDatasetAction class method) (galaxy.jobs.actions.post.RenameDatasetAction class method) (galaxy.jobs.actions.post.SetMetadataAction class method) (galaxy.jobs.actions.post.TagDatasetAction class method) (galaxy.workflow.modules.SimpleWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_consumer() (galaxy.web.framework.openid_manager.OpenIDManager method) get_containing_library_from_library_dataset() (in module galaxy.webapps.galaxy.controllers.library_common) get_content_type() (galaxy.web.framework.base.Response method) get_converted_dataset() (galaxy.model.DatasetInstance method) get_converted_dataset_deps() (galaxy.model.DatasetInstance method) get_converted_files_by_type() (galaxy.model.DatasetInstance method) get_converter_by_target_type() (galaxy.datatypes.registry.Registry method) get_converter_types() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) get_converters_by_datatype() (galaxy.datatypes.registry.Registry method) get_ctx_rev() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (in module tool_shed.util.shed_util_common) get_current() (galaxy.managers.histories.HistoryManager method) get_current_case() (galaxy.tools.parameters.grouping.Conditional method) get_current_cases() (galaxy.external_services.service.ExternalServiceActionsConditional method) get_current_form() (galaxy.webapps.galaxy.controllers.forms.Forms method) get_current_item() (galaxy.web.framework.helpers.grids.Grid method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid method) (tool_shed.grids.admin_grids.UserGrid method) get_current_repository_metadata_for_changeset_revision() (in module tool_shed.util.shed_util_common) get_current_roles() (galaxy.managers.folders.FolderManager method) (galaxy.managers.libraries.LibraryManager method) get_current_thread_object_dict() (in module galaxy.util.heartbeat) get_current_user_roles() (galaxy.jobs.deferred.FakeTrans method) (galaxy.managers.context.ProvidesUserContext method) get_data() (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy.visualization.data_providers.basic.ColumnDataProvider method) (galaxy.visualization.data_providers.phyloviz.PhylovizDataProvider method) get_data_inputs() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) (tool_shed.util.workflow_util.RepoToolModule method) get_data_outputs() (galaxy.workflow.modules.InputDataCollectionModule method) (galaxy.workflow.modules.InputDataModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) (tool_shed.util.workflow_util.RepoToolModule method) get_database_engine_options() (in module galaxy.config) (in module galaxy.webapps.reports.config) (in module galaxy.webapps.tool_shed.config) get_dataset_collection() (galaxy.managers.collections.DatasetCollectionManager method) get_dataset_collection_instance() (galaxy.managers.collections.DatasetCollectionManager method) get_dataset_filename() (in module galaxy.tools.imp_exp.export_history) get_dataset_finish_context() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) get_dataset_metadata_key() (galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper method) get_dataset_state() (galaxy.model.DatasetInstance method) get_datasources() (galaxy.model.DatasetInstance method) get_datatype() (galaxy.tools.parameters.grouping.UploadDataset method) get_datatype_by_extension() (galaxy.datatypes.registry.Registry method) get_datatype_class_by_name() (galaxy.datatypes.registry.Registry method) get_datatype_ext() (galaxy.tools.parameters.grouping.UploadDataset method) get_dbkey() (galaxy.model.DatasetInstance method) get_dbkeys() (galaxy.visualization.genomes.Genomes method) get_decimal_quality_scores() (galaxy_utils.sequence.fastq.fastqSequencingRead method) get_decimal_range() (galaxy_utils.sequence.fastq.fastqAggregator method) get_default_cache() (in module pkg_resources) get_default_history_by_trans() (galaxy.tools.DataManagerTool method) (galaxy.tools.Tool method) get_dependencies() (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) get_dependency_name() (galaxy.tools.parameters.dynamic_options.DataMetaFilter method) (galaxy.tools.parameters.dynamic_options.Filter method) (galaxy.tools.parameters.dynamic_options.ParamValueFilter method) (galaxy.tools.parameters.dynamic_options.UniqueValueFilter method)

get_dependency_names() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_destination() (galaxy.jobs.JobConfiguration method) get_destinations() (galaxy.jobs.JobConfiguration method) get_disabled_str() (galaxy.web.form_builder.BaseField method) get_disk_size() (galaxy.model.History method) get_disk_size_bytes (galaxy.model.History attribute) get_disk_usage() (galaxy.model.GalaxySession method) (galaxy.model.User method) (galaxy.webapps.reports.controllers.system.System method) (galaxy.webapps.tool_shed.model.User method) get_display_application() (galaxy.datatypes.data.Data method) get_display_applications() (galaxy.model.DatasetInstance method) get_display_applications_by_dataset() (galaxy.datatypes.data.Data method) get_display_label() (galaxy.datatypes.data.Data method) get_display_links() (galaxy.datatypes.data.Data method) get_display_name() (galaxy.model.HasName method) get_display_sites() (galaxy.datatypes.registry.Registry method) get_display_text() (galaxy.web.form_builder.HistoryField method) (galaxy.web.form_builder.LibraryField method) (galaxy.web.form_builder.WorkflowMappingField method) get_display_types() (galaxy.datatypes.data.Data method) get_display_url() (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) get_distribution() (in module pkg_resources) get_download_url_for_platform() (in module tool_shed.util.tool_dependency_util) get_editor_iframe() (galaxy.webapps.galaxy.controllers.page.PageController method) get_elements() (galaxy.util.topsort.CycleError method) get_embed_html_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) get_empty_field_by_name() (galaxy.tools.data.ToolDataTable method) get_entries() (galaxy.tools.data.TabularToolDataTable method) get_entry() (galaxy.tools.data.TabularToolDataTable method) (galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager method) get_entry_info() (in module pkg_resources) (pkg_resources.Distribution method) get_entry_map() (in module pkg_resources) (pkg_resources.Distribution method) get_env() (in module galaxy.eggs) get_env_setup_clause() (galaxy.jobs.JobWrapper method) get_errors() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_estimated_display_viewport() (galaxy.datatypes.interval.BedGraph method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) get_exit_code() (galaxy.jobs.TaskWrapper method) get_external_output_metadata() (galaxy.model.Job method) (galaxy.model.Task method) get_external_service() (galaxy.model.RequestType method) get_external_service_type() (galaxy.model.ExternalService method) (galaxy.webapps.galaxy.controllers.external_service.ExternalService method) get_external_services_for_manual_data_transfer() (galaxy.model.RequestType method) get_externally_referenced_paths() (galaxy.tools.Tool class method) get_extra_files_path() (galaxy.model.Dataset method) get_fasta_header() (in module galaxy.tools.util.maf_utilities) get_field() (galaxy.tools.data.TabularToolDataTable method) get_field_by_name_for_value() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_fields() (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_fields_by_value() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_file_base_name() (galaxy.tools.parameters.grouping.UploadDataset method) get_file_contents() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_file_details() (galaxy.webapps.galaxy.controllers.requests_admin.RequestsAdmin method) get_file_name() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) get_file_peek() (galaxy.datatypes.genetics.RexpBase method) (in module galaxy.datatypes.data) get_file_size() (in module galaxy.util) get_file_type() (galaxy.tools.parameters.grouping.UploadDataset method) get_filename() (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) get_filename_for_source() (galaxy.tools.data.TabularToolDataTable method) get_files() (galaxy.tools.data.TabularToolDataField method) get_filesize_map() (galaxy.tools.data.TabularToolDataField method) get_filter() (galaxy.web.framework.helpers.grids.CommunityTagsColumn method) (galaxy.web.framework.helpers.grids.IndividualTagsColumn method) (galaxy.web.framework.helpers.grids.TextColumn method) get_fingerprint() (galaxy.tools.data.TabularToolDataField method) get_folder_dict() (galaxy.managers.folders.FolderManager method) get_form_template() (in module galaxy.jobs.actions.post) get_form_values() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) get_forms() (galaxy.jobs.actions.post.ActionBox class method) get_func_list() (in module galaxy.web.framework.middleware.profile) get_functional_test_rss() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_galaxy_session() (galaxy.jobs.deferred.FakeTrans method) get_group() (galaxy.web.base.controller.BaseController method) (in module galaxy.web.base.controllers.admin) get_handler() (galaxy.jobs.JobConfiguration method) (galaxy.model.Job method) get_hda() (galaxy.web.base.controller.UsesVisualizationMixin method) get_hda_or_ldda() (galaxy.web.base.controller.UsesVisualizationMixin method) get_headers() (in module galaxy.datatypes.sniff) (in module tool_shed.util.tool_util) get_history_datasets() (galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper method) get_hook() (galaxy.tools.Tool method) get_html() (galaxy.datatypes.metadata.ColumnParameter method) (galaxy.datatypes.metadata.DBKeyParameter method) (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.datatypes.metadata.PythonObjectParameter method) (galaxy.datatypes.metadata.RangeParameter method) (galaxy.datatypes.metadata.SelectParameter method) (galaxy.model.UserAddress method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.web.form_builder.AddressField method) (galaxy.web.form_builder.BaseField method) (galaxy.web.form_builder.CheckboxField method) (galaxy.web.form_builder.DrillDownField method) (galaxy.web.form_builder.FTPFileField method) (galaxy.web.form_builder.FileField method) (galaxy.web.form_builder.HiddenField method) (galaxy.web.form_builder.HistoryField method) (galaxy.web.form_builder.LibraryField method) (galaxy.web.form_builder.PasswordField method) (galaxy.web.form_builder.SelectField method) (galaxy.web.form_builder.SwitchingSelectField method) (galaxy.web.form_builder.TextArea method) (galaxy.web.form_builder.TextField method) (galaxy.web.form_builder.WorkflowField method) (galaxy.web.form_builder.WorkflowMappingField method) get_html_by_name() (galaxy.datatypes.metadata.MetadataCollection method) get_html_checkboxes() (galaxy.web.form_builder.SelectField method) get_html_default() (galaxy.web.form_builder.SelectField method) get_html_field() (galaxy.datatypes.metadata.ColumnParameter method) (galaxy.datatypes.metadata.DBKeyParameter method) (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.datatypes.metadata.PythonObjectParameter method) (galaxy.datatypes.metadata.RangeParameter method) (galaxy.datatypes.metadata.SelectParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColorToolParameter method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter method) (galaxy.tools.parameters.basic.HiddenDataToolParameter method) (galaxy.tools.parameters.basic.HiddenToolParameter method) (galaxy.tools.parameters.basic.IntegerToolParameter method) (galaxy.tools.parameters.basic.LibraryDatasetToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.TextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) get_html_radio() (galaxy.web.form_builder.SelectField method) get_id() (galaxy.model.Job method) (galaxy.model.Task method) (in module galaxy.webapps.galaxy.api.genomes) get_id_col_in_item_tag_assoc_table() (galaxy.managers.tags.TagManager method) get_id_tag() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) get_ids() (galaxy.web.framework.helpers.grids.Grid method) get_ids_of_tool_shed_repositories_being_installed() (in module tool_shed.util.shed_util_common) get_image_ext() (in module galaxy.datatypes.util.image_util) get_imported() (galaxy.model.Job method) get_importer() (in module pkg_resources) get_incoming_value() (in module galaxy.tools) get_index() (galaxy.tools.test.RootParamContext method) get_info() (galaxy.model.Job method) (galaxy.model.LibraryDataset method) (galaxy.model.Task method) get_info_association() (galaxy.model.Library method) (galaxy.model.LibraryDatasetDatasetAssociation method) (galaxy.model.LibraryFolder method) get_inital_values() (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) get_initial_value() (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColorToolParameter method) (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter method) (galaxy.tools.parameters.basic.HiddenDataToolParameter method) (galaxy.tools.parameters.basic.HiddenToolParameter method) (galaxy.tools.parameters.basic.IntegerToolParameter method) (galaxy.tools.parameters.basic.LibraryDatasetToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.TextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.grouping.Conditional method) (galaxy.tools.parameters.grouping.Group method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.tools.parameters.grouping.UploadDataset method) get_initial_value_from_history_prevent_repeats() (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) get_input_dataset_fnames() (galaxy.jobs.JobWrapper method) get_input_datasets() (galaxy.model.Job method) get_input_files() (galaxy.jobs.runners.lwr.LwrJobRunner method) get_input_fnames() (galaxy.jobs.JobWrapper method) get_input_library_datasets() (galaxy.model.Job method) get_input_paths() (galaxy.jobs.JobWrapper method) get_interesting_stack_frame() (galaxy.util.heartbeat.Heartbeat method) get_invocation() (galaxy.managers.workflows.WorkflowsManager method) get_invocation_step() (galaxy.managers.workflows.WorkflowsManager method) get_item() (galaxy.web.base.controller.SharableMixin method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) get_item_actions() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) (galaxy.webapps.tool_shed.security.RBACAgent method) get_item_and_stuff() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) get_item_annotation_obj() (galaxy.model.item_attrs.UsesAnnotations method) get_item_annotation_str() (galaxy.model.item_attrs.UsesAnnotations method) get_item_content_async() (galaxy.web.base.controller.SharableMixin method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) get_item_extended_metadata_obj() (galaxy.web.base.controller.UsesExtendedMetadataMixin method) get_iterator() (galaxy.visualization.data_providers.basic.BaseDataProvider method) get_job() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) (in module galaxy.webapps.reports.controllers.jobs) get_job_destination() (galaxy.jobs.mapper.JobRunnerMapper method) (galaxy.tools.Tool method) get_job_file() (galaxy.jobs.runners.BaseJobRunner method) get_job_handler() (galaxy.tools.Tool method) get_job_runner() (galaxy.jobs.JobWrapper method) get_job_runner_external_id() (galaxy.model.Job method) (galaxy.model.Task method) get_job_runner_name() (galaxy.model.Job method) (galaxy.model.Task method) get_job_runner_plugins() (galaxy.jobs.JobConfiguration method) get_job_runner_url() (galaxy.jobs.JobWrapper method) get_job_tool_configurations() (galaxy.jobs.JobConfiguration method) get_label() (galaxy.tools.parameters.basic.HiddenToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) get_last_check() (galaxy.model.DeferredJob method) get_latest_changeset_revision() (in module tool_shed.util.metadata_util) get_latest_downloadable_changeset_revision() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (in module tool_shed.util.shed_util_common) get_latest_downloadable_repository_metadata() (in module tool_shed.grids.util) get_latest_downloadable_repository_metadata_if_it_has_test_install_errors() (in module tool_shed.grids.util) get_latest_downloadable_repository_metadata_if_it_includes_tools() (in module tool_shed.grids.util) get_latest_installable_revision() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) get_latest_repository_metadata() (in module tool_shed.grids.util) (in module tool_shed.util.metadata_util) get_latest_repository_metadata_if_it_includes_invalid_tools() (in module tool_shed.grids.util) get_legacy_sites_by_build() (galaxy.datatypes.registry.Registry method) get_legal_values() (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.GenomeBuildParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) get_legitimate_roles() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_length_counts() (galaxy_utils.sequence.fastq.fastqAggregator method) get_library() (galaxy.web.base.controller.UsesLibraryMixin method) get_library_dataset() (galaxy.web.base.controller.UsesLibraryMixinItems method) get_library_dataset_dataset_association() (galaxy.web.base.controller.UsesLibraryMixinItems method) get_library_dict() (galaxy.managers.libraries.LibraryManager method) get_library_folder() (galaxy.web.base.controller.UsesLibraryMixinItems method) get_link() (galaxy.datatypes.display_applications.application.DisplayApplication method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.framework.helpers.grids.PublicURLColumn method) (galaxy.web.framework.helpers.grids.SharingStatusColumn method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid.HistoryListNameColumn method) get_manage_permissions_roles() (galaxy.model.Dataset method) (galaxy.model.LibraryDatasetDatasetAssociation method) get_manage_roles() (galaxy.managers.libraries.LibraryManager method) get_mapping_by_name() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer class method) get_max_optional_metadata_filesize() (galaxy.datatypes.data.Data method) get_max_read_length() (galaxy_utils.sequence.fastq.fastqAggregator method) get_message_for_no_shed_tool_config() (in module galaxy.webapps.galaxy.api.tool_shed_repositories) get_metadata() (galaxy.model.DatasetInstance method) (pkg_resources.FileMetadata method) (pkg_resources.IMetadataProvider method) (pkg_resources.NullProvider method) get_metadata_dataset() (galaxy.model.DatasetInstance method) get_metadata_file() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) get_metadata_lines() (pkg_resources.FileMetadata method) (pkg_resources.IMetadataProvider method) (pkg_resources.NullProvider method) get_mime() (galaxy.datatypes.binary.Binary method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.Rgenetics method) (galaxy.datatypes.genetics.rgTabList method) (galaxy.datatypes.images.Gmaj method) (galaxy.datatypes.images.Html method) (galaxy.model.DatasetInstance method) get_mimetype_by_extension() (galaxy.datatypes.registry.Registry method) get_modify_roles() (galaxy.managers.libraries.LibraryManager method) get_monitor_id() (in module galaxy.webapps.reports.controllers.jobs) get_most_recently_used_tool_async() (galaxy.webapps.galaxy.controllers.user.User method) get_mutable_output_fnames() (galaxy.jobs.JobWrapper method) get_name() (galaxy.model.LibraryDataset method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_name_and_link_async() (galaxy.web.base.controller.SharableMixin method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) get_named_fields_list() (galaxy.tools.data.TabularToolDataTable method) get_native_spec() (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) get_new_guid() (galaxy.web.security.SecurityHelper method) get_new_module_info() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) get_new_track_config() (galaxy.web.base.controller.UsesVisualizationMixin method) get_next_downloadable_changeset_revision() (in module tool_shed.util.shed_util_common) get_next_prior_import_or_install_required_dict_entry() (in module tool_shed.util.shed_util_common) get_non_shed_tool_panel_configs() (in module tool_shed.util.common_util) get_object() (galaxy.web.base.controller.BaseAPIController method) (galaxy.web.base.controller.BaseController method) (galaxy.web.base.controller.BaseUIController method) (in module galaxy.managers.base) get_object_url() (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) get_open_tempfile() (galaxy.tools.util.maf_utilities.TempFileHandler method) get_options() (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.GenomeBuildParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_or_create_api_key() (galaxy.managers.api_keys.ApiKeyManager method) get_ordered_installable_revisions() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method) get_ordered_metadata_changeset_revisions() (in module tool_shed.util.shed_util_common) get_oriented_chopped_blocks_for_region() (in module galaxy.tools.util.maf_utilities) get_oriented_chopped_blocks_with_index_offset_for_region() (in module galaxy.tools.util.maf_utilities) get_output_datasets() (galaxy.model.Job method) get_output_destination() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) get_output_file_id() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) get_output_filenames_by_dataset() (galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper method) get_output_files() (galaxy.jobs.runners.lwr.LwrJobRunner method) get_output_fnames() (galaxy.jobs.JobWrapper method) get_output_hdas_and_fnames() (galaxy.jobs.JobWrapper method) get_output_library_datasets() (galaxy.model.Job method) get_output_name() (galaxy.tools.actions.DefaultToolAction method) get_output_sizes() (galaxy.jobs.JobWrapper method) get_page() (galaxy.webapps.galaxy.controllers.page.PageController method) get_paired_identifier() (galaxy_utils.sequence.fastq.fastqJoiner method) get_pairlist() (galaxy.util.topsort.CycleError method) get_panel_section() (galaxy.tools.Tool method) get_parallelism() (galaxy.jobs.JobWrapper method) get_param() (galaxy.tools.Tool method) get_param_dict() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) get_param_filename() (galaxy.model.Job method) get_param_html_map() (galaxy.tools.Tool method) get_param_name_by_url() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) get_param_value() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) get_param_values() (galaxy.model.Job method) (galaxy.model.Task method) get_parameters() (galaxy.model.Job method) (galaxy.model.Task method) get_params() (galaxy.model.Job method) (galaxy.web.params.BaseParamParser method) get_parent() (galaxy.datatypes.metadata.MetadataCollection method) get_partial() (galaxy.util.topsort.CycleError method) get_path_paste_uploaded_datasets() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) get_peek() (galaxy.datatypes.genetics.RexpBase method) get_percent() (galaxy.quota.NoQuotaAgent method) (galaxy.quota.QuotaAgent method) get_permissions() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (galaxy.webapps.galaxy.api.folders.FoldersController method) (galaxy.webapps.galaxy.api.libraries.LibrariesController method) get_permitted_actions() (in module galaxy.security) (in module galaxy.webapps.tool_shed.security) get_permitted_libraries() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_phecols() (galaxy.datatypes.genetics.RexpBase method) get_pheno() (galaxy.datatypes.genetics.RexpBase method) get_platform() (in module pkg_resources) get_platform_info_dict() (in module tool_shed.util.tool_dependency_util) get_platforms() (galaxy.eggs.dist.DistScrambleCrate method) get_post_job_actions() (galaxy.model.Job method) (galaxy.workflow.modules.ToolModule method) get_precreated_dataset() (in module galaxy.tools.actions.upload_common) get_precreated_datasets() (in module galaxy.tools.actions.upload_common) get_pred_counts() (galaxy.util.topsort.CycleError method) get_preds() (galaxy.util.topsort.CycleError method) get_prepare_input_files_cmd() (galaxy.model.Task method) get_prepare_steps() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) get_previous_metadata_changeset_revision() (in module tool_shed.util.metadata_util) get_previous_repository_reviews() (in module tool_shed.util.review_util) get_prior_import_or_install_required_dict() (in module tool_shed.util.shed_util_common) get_private_user_role() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) (galaxy.webapps.tool_shed.security.RBACAgent method) get_protocol_from_tool_shed_url() (in module tool_shed.util.common_util) get_provider() (in module pkg_resources) get_published_visualizations() (galaxy.web.base.controller.UsesVisualizationMixin method) get_quota() (galaxy.quota.NoQuotaAgent method) (galaxy.quota.QuotaAgent method) (galaxy.web.base.controller.UsesQuotaMixin method) (in module galaxy.web.base.controllers.admin) get_quota_params() (galaxy.web.params.QuotaParamParser method) get_random_bytes() (in module galaxy.web.security) get_raw_data() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) get_read_count() (galaxy_utils.sequence.fastq.fastqAggregator method) get_read_count_for_column() (galaxy_utils.sequence.fastq.fastqAggregator method) get_readme_file_names() (in module tool_shed.util.readme_util) get_readme_files() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_readme_files_dict_for_display() (in module tool_shed.util.readme_util) get_ref() (galaxy.external_services.service.ExternalServiceActionsGroupWhen method) (galaxy.tools.parameters.output.ToolOutputActionConditionalWhen method) get_region_alignment() (in module galaxy.tools.util.maf_utilities) get_repo_info_tuple_contents() (in module tool_shed.util.shed_util_common) get_reports() (galaxy.util.debugging.SimpleProfiler method) get_repository_and_repository_dependencies_from_repo_info_dict() (in module tool_shed.util.shed_util_common) get_repository_by_id() (in module tool_shed.util.shed_util_common) get_repository_by_name() (in module tool_shed.util.shed_util_common) get_repository_by_name_and_owner() (in module tool_shed.util.shed_util_common) get_repository_categories() (in module tool_shed.util.shed_util_common) get_repository_components_for_installation() (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) get_repository_dependencies() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (in module tool_shed.util.common_util) get_repository_dependency_tups_from_repository_metadata() (in module tool_shed.util.metadata_util) get_repository_dependency_types() (in module tool_shed.util.shed_util_common) get_repository_file_contents() (in module tool_shed.util.shed_util_common) get_repository_files() (in module tool_shed.util.shed_util_common) get_repository_for_dependency_relationship() (in module tool_shed.util.shed_util_common) get_repository_from_refresh_on_change() (in module tool_shed.util.shed_util_common) get_repository_id() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_repository_ids_requiring_prior_import_or_install() (in module tool_shed.util.shed_util_common) get_repository_in_tool_shed() (in module tool_shed.util.shed_util_common) get_repository_information() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_repository_metadata_by_changeset_revision() (in module tool_shed.util.shed_util_common) get_repository_metadata_by_id() (in module tool_shed.util.metadata_util) get_repository_metadata_by_repository_id_changeset_revision() (in module tool_shed.util.metadata_util) get_repository_metadata_revisions_for_review() (in module tool_shed.util.metadata_util) get_repository_owner() (in module tool_shed.util.shed_util_common) get_repository_owner_from_clone_url() (in module tool_shed.util.shed_util_common) get_repository_query() (in module tool_shed.util.shed_util_common) get_repository_reviewer_role() (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) get_repository_revision_install_info() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method) get_request() (in module galaxy.webapps.reports.controllers.sample_tracking) get_required_enctype() (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) get_required_repo_info_dict() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_resource_filename() (pkg_resources.IResourceProvider method) (pkg_resources.NullProvider method) (pkg_resources.ZipProvider method) get_resource_group() (galaxy.jobs.JobToolConfiguration method) get_resource_stream() (pkg_resources.DefaultProvider method) (pkg_resources.IResourceProvider method) (pkg_resources.NullProvider method) get_resource_string() (pkg_resources.IResourceProvider method) (pkg_resources.NullProvider method) get_review() (in module tool_shed.util.review_util) get_review_by_repository_id_changeset_revision_user_id() (in module tool_shed.util.review_util) get_reviews_by_repository_id_changeset_revision() (in module tool_shed.util.review_util) get_role() (galaxy.web.base.controller.BaseController method) (in module galaxy.web.base.controllers.admin) get_roles_for_action() (galaxy.security.GalaxyRBACAgent method) get_runtime_input_dicts() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_runtime_inputs() (galaxy.workflow.modules.InputDataCollectionModule method) (galaxy.workflow.modules.InputDataModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.WorkflowModule method) get_runtime_state() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.PauseModule method) get_sample() (galaxy.model.Request method) get_saved_form() (galaxy.webapps.galaxy.controllers.forms.Forms method) get_score_at_position_for_column() (galaxy_utils.sequence.fastq.fastqAggregator method) get_score_list_for_column() (galaxy_utils.sequence.fastq.fastqAggregator method) get_score_max_for_column() (galaxy_utils.sequence.fastq.fastqAggregator method) get_score_min_for_column() (galaxy_utils.sequence.fastq.fastqAggregator method) get_score_sum_for_column() (galaxy_utils.sequence.fastq.fastqAggregator method) get_selected() (galaxy.web.form_builder.SelectField method) get_sequence() (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.SplicedAlignment method) (galaxy_utils.sequence.fastq.fastqCSSangerRead method) (galaxy_utils.sequence.fastq.fastqSequencingRead method) get_sequence_reverse_complement() (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.SplicedAlignment method) get_sequences_per_file() (galaxy.datatypes.sequence.Sequence static method) get_server_dir_uploaded_datasets() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) get_session() (galaxy.web.framework.openid_manager.OpenIDManager method) get_session_id() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) get_sharing_roles() (galaxy.security.GalaxyRBACAgent method) get_short_str() (galaxy.jobs.actions.post.ActionBox class method) (galaxy.jobs.actions.post.ChangeDatatypeAction class method) (galaxy.jobs.actions.post.ColumnSetAction class method) (galaxy.jobs.actions.post.DefaultJobAction class method) (galaxy.jobs.actions.post.DeleteDatasetAction class method) (galaxy.jobs.actions.post.DeleteIntermediatesAction class method) (galaxy.jobs.actions.post.EmailAction class method) (galaxy.jobs.actions.post.HideDatasetAction class method) (galaxy.jobs.actions.post.RenameDatasetAction class method) (galaxy.jobs.actions.post.TagDatasetAction class method) get_showable_folders() (galaxy.security.GalaxyRBACAgent method) get_single_filter() (galaxy.web.framework.helpers.grids.BooleanColumn method) (galaxy.web.framework.helpers.grids.IntegerColumn method) (galaxy.web.framework.helpers.grids.OwnerAnnotationColumn method) (galaxy.web.framework.helpers.grids.TextColumn method) get_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) get_sorted_accessible_library_items() (in module galaxy.webapps.galaxy.controllers.library_common) get_species_in_block() (in module galaxy.tools.util.maf_utilities) get_species_in_maf() (in module galaxy.tools.util.maf_utilities) get_species_names() (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.SplicedAlignment method) get_spliced_region_alignment() (in module galaxy.tools.util.maf_utilities) get_split_commands_sequential() (galaxy.datatypes.sequence.Sequence static method) get_split_commands_with_toc() (galaxy.datatypes.sequence.Sequence static method) get_sreg() (galaxy.web.framework.openid_manager.OpenIDManager method) get_starts_ends_fields_from_gene_bed() (in module galaxy.tools.util.maf_utilities) get_state() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.jobs.transfer_manager.TransferManager method) (galaxy.model.Job method) (galaxy.model.Task method) (galaxy.workflow.modules.SimpleWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_static_param_values() (galaxy.tools.Tool method) get_stderr() (galaxy.model.Task method) get_stdout() (galaxy.model.Task method) get_store_usage_percent() (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.ObjectStore method) get_stored_workflow() (galaxy.web.base.controller.UsesStoredWorkflowMixin method) get_stored_workflow_steps() (galaxy.web.base.controller.UsesStoredWorkflowMixin method) get_succs() (galaxy.util.topsort.CycleError method) get_suite() (in module galaxy.tools.parameters.validation) (in module galaxy.web.form_builder) get_summary_statistics_for_column() (galaxy_utils.sequence.fastq.fastqAggregator method) get_tables() (galaxy.tools.data.ToolDataTableManager method) get_tag_assoc_class() (galaxy.managers.tags.TagManager method) get_tag_by_id() (galaxy.managers.tags.TagManager method) get_tag_by_name() (galaxy.managers.tags.TagManager method) get_tag_handler() (galaxy.web.base.controller.UsesTagsMixin method) get_tagging_elt_async() (galaxy.webapps.galaxy.controllers.tag.TagsController method) get_tags_str() (galaxy.managers.tags.TagManager method) get_task() (galaxy.jobs.TaskWrapper method) get_task_runner_external_id() (galaxy.model.Task method) get_task_runner_name() (galaxy.model.Task method) get_tasks() (galaxy.model.Job method) get_template_widgets() (galaxy.model.Library method) (galaxy.model.LibraryDatasetDatasetAssociation method) (galaxy.model.LibraryFolder method) (galaxy.model.RequestType method) (galaxy.model.Sample method) get_test_fname() (in module galaxy.datatypes.data) (in module galaxy.datatypes.sniff) get_tld() (galaxy.eggs.scramble.ScrambleEgg method) get_tool_def() (galaxy.web.base.controller.UsesVisualizationMixin method) get_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (in module tool_shed.util.common_util) get_tool_dependencies_config_contents() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_tool_dependency() (in module tool_shed.util.tool_dependency_util) get_tool_dependency_by_name_type_repository() (in module tool_shed.util.tool_dependency_util) get_tool_dependency_by_name_version_type() (in module tool_shed.util.tool_dependency_util) get_tool_dependency_by_name_version_type_repository() (in module tool_shed.util.tool_dependency_util) get_tool_dependency_ids() (in module tool_shed.util.tool_dependency_util) get_tool_dependency_install_dir() (in module tool_shed.util.tool_dependency_util) get_tool_id() (galaxy.model.Job method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_tool_panel_config_tool_path_install_dir() (in module tool_shed.util.shed_util_common) get_tool_path_by_shed_tool_conf_filename() (in module tool_shed.util.shed_util_common) get_tool_path_install_dir() (in module tool_shed.util.tool_util) get_tool_provided_job_metadata() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) get_tool_resource_parameters() (galaxy.jobs.JobConfiguration method) get_tool_shed_from_clone_url() (in module tool_shed.util.shed_util_common) get_tool_shed_repository_by_id() (in module tool_shed.util.shed_util_common) get_tool_shed_repository_by_shed_name_owner_changeset_revision() (in module tool_shed.util.shed_util_common) get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision() (in module tool_shed.util.shed_util_common) get_tool_shed_repository_ids() (in module tool_shed.util.common_util) get_tool_shed_repository_install_dir() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) get_tool_shed_repository_status_label() (in module tool_shed.util.shed_util_common) get_tool_shed_status_for_installed_repository() (in module tool_shed.util.shed_util_common) get_tool_shed_url_from_tool_shed_registry() (in module tool_shed.util.common_util) get_tool_tags() (galaxy.managers.tags.TagManager method) get_tool_version() (galaxy.model.Job method) (galaxy.workflow.modules.ToolModule method) get_tool_versions() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_toolbox() (galaxy.managers.context.ProvidesAppContext method) (galaxy.web.base.controller.BaseController method) get_tooltip() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_total_job_count_per_destination() (galaxy.jobs.handler.JobHandlerQueue method) get_total_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) get_track_resolution() (galaxy.datatypes.coverage.LastzCoverage method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) get_track_window() (galaxy.datatypes.coverage.LastzCoverage method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) get_type() (galaxy.workflow.modules.WorkflowModule method) get_type_class() (galaxy.webapps.tool_shed.model.Repository method) get_untransferred_dataset_size() (galaxy.model.Sample method) get_updated_changeset_revisions() (in module tool_shed.util.shed_util_common) get_updated_changeset_revisions_from_tool_shed() (in module tool_shed.util.shed_util_common) get_updated_repository_information() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_upload_metadata_params() (galaxy.datatypes.registry.Registry method) get_uploaded_datasets() (galaxy.tools.parameters.grouping.UploadDataset method) (in module galaxy.tools.actions.upload_common) get_url_args() (galaxy.web.framework.helpers.grids.DisplayByUsernameAndSlugGridOperation method) (galaxy.web.framework.helpers.grids.GridColumnFilter method) (galaxy.web.framework.helpers.grids.GridOperation method) get_usage() (galaxy.quota.NoQuotaAgent method) get_user() (galaxy.model.Job method) (galaxy.web.base.controller.BaseController method) (in module galaxy.web.base.controllers.admin) (in module tool_shed.util.shed_util_common) get_user_by_username() (in module galaxy.web.base.controllers.admin) (in module tool_shed.util.shed_util_common) get_user_id() (galaxy.model.Job method) get_user_item_rating() (galaxy.model.item_attrs.UsesItemRatings method) get_user_job_count() (galaxy.jobs.handler.JobHandlerQueue method) get_user_job_count_per_destination() (galaxy.jobs.handler.JobHandlerQueue method) get_user_quotas() (galaxy.quota.NoQuotaAgent method) (galaxy.quota.QuotaAgent method) get_user_tags_used() (galaxy.web.base.controller.UsesTagsMixin method) get_valid_by_name() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer class method) get_valid_formats() (galaxy_utils.sequence.fastq.fastqAggregator method) get_valid_roles() (galaxy.security.GalaxyRBACAgent method) get_value() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationTemplateParameter method) (galaxy.external_services.parameters.ExternalServiceParameter method) (galaxy.external_services.parameters.ExternalServiceTemplateParameter method) (galaxy.tools.parameters.output.FromDataTableOutputActionOption method) (galaxy.tools.parameters.output.FromFileToolOutputActionOption method) (galaxy.tools.parameters.output.FromParamToolOutputActionOption method) (galaxy.tools.parameters.output.NullToolOutputActionOption method) (galaxy.tools.parameters.output.ToolOutputActionOption method) (galaxy.web.framework.helpers.grids.CommunityRatingColumn method) (galaxy.web.framework.helpers.grids.CommunityTagsColumn method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.framework.helpers.grids.IndividualTagsColumn method) (galaxy.web.framework.helpers.grids.OwnerAnnotationColumn method) (galaxy.web.framework.helpers.grids.OwnerColumn method) (galaxy.web.framework.helpers.grids.SharingStatusColumn method) (galaxy.web.framework.helpers.grids.StateColumn method) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid.RolesColumn method) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid.StatusColumn method) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid.UsersColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.AmountColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.DescriptionColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.GroupsColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.StatusColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.UsersColumn method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid.DescriptionColumn method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid.GroupsColumn method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid.StatusColumn method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid.TypeColumn method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid.UsersColumn method) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid.ToolIdColumn method) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid.ToolVersionsColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.ActivatedColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.EmailColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.ExternalColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.GroupsColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.LastLoginColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.RolesColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.StatusColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.TimeCreatedColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.UserNameColumn method) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid.HistoryColumn method) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid.StatusColumn method) (galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid.ExternalServiceTypeColumn method) (galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.forms.FormsGrid.DescriptionColumn method) (galaxy.webapps.galaxy.controllers.forms.FormsGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.forms.FormsGrid.TypeColumn method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid.DatasetsByStateColumn method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid.DeletedColumn method) (galaxy.webapps.galaxy.controllers.history.NameColumn method) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid.DatasetsByStateColumn method) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid.SharedByColumn method) (galaxy.webapps.galaxy.controllers.library.LibraryListGrid.DescriptionColumn method) (galaxy.webapps.galaxy.controllers.library.LibraryListGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid.DescriptionColumn method) (galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid.StatusColumn method) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.page.PageListGrid.URLColumn method) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid.DescriptionColumn method) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid.ExternalServiceColumn method) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid.RequestFormColumn method) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid.SampleFormColumn method) (galaxy.webapps.galaxy.controllers.requests_admin.AdminRequestsGrid.UserColumn method) (galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid.ExternalServiceColumn method) (galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid.SizeColumn method) (galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid.StatusColumn method) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid.DescriptionColumn method) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid.SamplesColumn method) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid.StateColumn method) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid.TypeColumn method) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid.StepsColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.CreateTimeColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.JobIdColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.StateColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.ToolColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.UserColumn method) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid.CreateTimeColumn method) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid.RequestNameColumn method) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid.UserColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.CreateTimeColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.UserColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.WorkflowNameColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.DescriptionColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.NameColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.OwnerColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.RevisionColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.StatusColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.ToolShedColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.ToolShedStatusColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid.DescriptionColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid.NameColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid.OwnerColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid.RevisionColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid.StatusColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid.NameColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid.StatusColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid.TypeColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid.VersionColumn method) (tool_shed.grids.admin_grids.AdminRepositoryGrid.DeletedColumn method) (tool_shed.grids.admin_grids.GroupGrid.NameColumn method) (tool_shed.grids.admin_grids.GroupGrid.RolesColumn method) (tool_shed.grids.admin_grids.GroupGrid.StatusColumn method) (tool_shed.grids.admin_grids.GroupGrid.UsersColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.DatatypesColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.DeletedColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.DeprecatedColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.IdColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.MaliciousColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.NameColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.OwnerColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.RevisionColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.ToolsColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.WorkflowsColumn method) (tool_shed.grids.admin_grids.RoleGrid.DescriptionColumn method) (tool_shed.grids.admin_grids.RoleGrid.GroupsColumn method) (tool_shed.grids.admin_grids.RoleGrid.NameColumn method) (tool_shed.grids.admin_grids.RoleGrid.RepositoriesColumn method) (tool_shed.grids.admin_grids.RoleGrid.StatusColumn method) (tool_shed.grids.admin_grids.RoleGrid.TypeColumn method) (tool_shed.grids.admin_grids.RoleGrid.UsersColumn method) (tool_shed.grids.admin_grids.UserGrid.ExternalColumn method) (tool_shed.grids.admin_grids.UserGrid.GroupsColumn method) (tool_shed.grids.admin_grids.UserGrid.LastLoginColumn method) (tool_shed.grids.admin_grids.UserGrid.RolesColumn method) (tool_shed.grids.admin_grids.UserGrid.StatusColumn method) (tool_shed.grids.admin_grids.UserGrid.UserLoginColumn method) (tool_shed.grids.admin_grids.UserGrid.UserNameColumn method) (tool_shed.grids.repository_grids.CategoryGrid.DescriptionColumn method) (tool_shed.grids.repository_grids.CategoryGrid.NameColumn method) (tool_shed.grids.repository_grids.CategoryGrid.RepositoriesColumn method) (tool_shed.grids.repository_grids.DatatypesGrid.DatatypesColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.DescriptionColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.NameColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.RevisionColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.UserColumn method) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid.InvalidToolConfigColumn method) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid.RequiredRepositoryColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.CategoryColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.DeprecatedColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.DescriptionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.EmailAlertsColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.HeadsColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.LatestInstallableRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.MetadataRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.NameColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.TipRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.ToolsFunctionallyCorrectColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.TypeColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.UserColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.ChangesetRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.DoNotTestColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.DownloadableColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.HasRepositoryDependenciesColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesDatatypesColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesToolDependenciesColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesToolsColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesWorkflowsColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.MaliciousColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.RepositoryNameColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.RepositoryOwnerColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.RepositoryTypeColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.TimeLastTestedColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.ToolsFunctionallyCorrectColumn method) (tool_shed.grids.repository_grids.ToolDependenciesGrid.ToolDependencyColumn method) (tool_shed.grids.repository_grids.ToolsGrid.ToolsColumn method) (tool_shed.grids.repository_grids.ValidCategoryGrid.RepositoriesColumn method) (tool_shed.grids.repository_grids.ValidRepositoryGrid.CategoryColumn method) (tool_shed.grids.repository_grids.ValidRepositoryGrid.InstallableRevisionColumn method) (tool_shed.grids.repository_review_grids.ComponentGrid.DescriptionColumn method) (tool_shed.grids.repository_review_grids.ComponentGrid.NameColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.ApprovedColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.RatingColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.ReviewersColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.WithReviewsRevisionColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn method) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid.RatingColumn method) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid.RepositoryDescriptionColumn method) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid.RepositoryNameColumn method) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid.RevisionColumn method) get_version_fields() (galaxy.tools.data.TabularToolDataTable method) get_version_string_path() (galaxy.jobs.JobWrapper method) get_visualization() (galaxy.web.base.controller.UsesVisualizationMixin method) get_visualization_config() (galaxy.web.base.controller.UsesVisualizationMixin method) get_visualization_dict() (galaxy.web.base.controller.UsesVisualizationMixin method) get_visualization_revision_dict() (galaxy.web.base.controller.UsesVisualizationMixin method) get_visualization_summary_dict() (galaxy.web.base.controller.UsesVisualizationMixin method) get_visualizations() (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Newick method) (galaxy.datatypes.data.Nexus method) (galaxy.datatypes.xml.Phyloxml method) (galaxy.model.DatasetInstance method) get_visualizations_by_user() (galaxy.web.base.controller.UsesVisualizationMixin method) get_visualizations_shared_with_user() (galaxy.web.base.controller.UsesVisualizationMixin method) get_web_api_action() (galaxy.external_services.actions.ExternalServiceWebAPIAction.ExternalServiceWebAPIActionRequest method) get_widgets() (galaxy.model.FormDefinition method) get_work_dir_outputs() (galaxy.jobs.runners.BaseJobRunner method) get_workflow() (in module galaxy.webapps.reports.controllers.workflows) get_workflow_data_inputs() (in module tool_shed.util.workflow_util) get_workflow_data_outputs() (in module tool_shed.util.workflow_util) get_workflow_from_dict() (in module tool_shed.util.workflow_util) get_workflow_module_name() (in module tool_shed.util.workflow_util) get_working_directory() (galaxy.model.Task method) getMissval() (in module galaxy.datatypes.converters.lped_to_pbed_converter) Gff (class in galaxy.datatypes.interval) Gff3 (class in galaxy.datatypes.interval) gff_attributes_to_str() (in module galaxy.datatypes.util.gff_util) GFFFeature (class in galaxy.datatypes.util.gff_util) GFFInterval (class in galaxy.datatypes.util.gff_util) GFFIntervalToBEDReaderWrapper (class in galaxy.datatypes.util.gff_util) GFFReaderWrapper (class in galaxy.datatypes.util.gff_util) Gif (class in galaxy.datatypes.images) global_actions (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid attribute) (galaxy.webapps.galaxy.controllers.requests_admin.AdminRequestsGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.ManageCategoryGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.EmailAlertsRepositoryGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) Gmaj (class in galaxy.datatypes.images) Grid (class in galaxy.web.framework.helpers.grids) grid_fields() (galaxy.model.FormDefinition method) GridAction (class in galaxy.web.framework.helpers.grids) GridColumn (class in galaxy.web.framework.helpers.grids) GridColumnFilter (class in galaxy.web.framework.helpers.grids) GridOperation (class in galaxy.web.framework.helpers.grids) groom_dataset_content() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.data.Data method) Group (class in galaxy.model) (class in galaxy.tools.parameters.grouping) (class in galaxy.webapps.tool_shed.model) group (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) group_assoc (galaxy.managers.roles.RoleManager attribute) group_id (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) group_list_grid (galaxy.web.base.controllers.admin.Admin attribute) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (galaxy.webapps.tool_shed.controllers.admin.AdminController attribute) group_title() (galaxy.tools.parameters.grouping.UploadDataset method) GroupAPIController (class in galaxy.webapps.galaxy.api.groups) GroupGrid (class in tool_shed.grids.admin_grids) GroupGrid.NameColumn (class in tool_shed.grids.admin_grids) GroupGrid.RolesColumn (class in tool_shed.grids.admin_grids) GroupGrid.StatusColumn (class in tool_shed.grids.admin_grids) GroupGrid.UsersColumn (class in tool_shed.grids.admin_grids) GroupListGrid (class in galaxy.webapps.galaxy.controllers.admin) GroupListGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.admin) GroupListGrid.RolesColumn (class in galaxy.webapps.galaxy.controllers.admin) GroupListGrid.StatusColumn (class in galaxy.webapps.galaxy.controllers.admin) GroupListGrid.UsersColumn (class in galaxy.webapps.galaxy.controllers.admin) GroupQuotaAssociation (class in galaxy.model) GroupRoleAssociation (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) GroupRolesAPIController (class in galaxy.webapps.galaxy.api.group_roles) groups (galaxy.webapps.tool_shed.model.Role attribute) groups() (galaxy.web.base.controllers.admin.Admin method) GroupUsersAPIController (class in galaxy.webapps.galaxy.api.group_users) Gtf (class in galaxy.datatypes.interval) guess_derived_permissions_for_datasets() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) guess_ext() (in module galaxy.datatypes.sniff) guess_galaxy_port() (galaxy.config.Configuration method)

H

H5 (class in galaxy.datatypes.binary) handle_action() (galaxy.external_services.actions.ExternalServiceAction method) handle_compressed_file() (in module galaxy.datatypes.sniff) handle_controller_exception() (galaxy.web.framework.base.WebApplication method) handle_data() (galaxy.webapps.galaxy.controllers.workflow.SingleTagContentsParser method) handle_datatypes_changed() (galaxy.tools.ToolBox method) handle_email_alerts() (in module tool_shed.util.shed_util_common) handle_found_index_file() (galaxy.tools.data.TabularToolDataTable method) handle_galaxy_url() (in module tool_shed.util.common_util) handle_incoming() (galaxy.jobs.actions.post.ActionBox class method) handle_input() (galaxy.tools.Tool method) handle_interrupted() (galaxy.tools.Tool method) handle_job_failure_exception() (galaxy.tools.Tool method) handle_library_params() (in module galaxy.tools.actions.upload_common) handle_missing_index_file() (in module tool_shed.util.tool_util) handle_operation() (galaxy.web.framework.helpers.grids.Grid method) handle_population_failed() (galaxy.model.DatasetCollection method) handle_request() (galaxy.web.framework.base.WebApplication method) (galaxy.webapps.tool_shed.controllers.hg.HgController method) handle_result() (galaxy.external_services.result_handlers.basic.ExternalServiceActionJQueryGridResultHandler method) (galaxy.external_services.result_handlers.basic.ExternalServiceActionJSONResultHandler method) (galaxy.external_services.result_handlers.basic.ExternalServiceActionResultHandler method) (galaxy.external_services.result_handlers.basic.ExternalServiceActionURLRedirectResultHandler method) handle_results() (galaxy.external_services.actions.PopulatedExternalServiceAction method) handle_single_execution() (galaxy.tools.Tool method) handle_stop() (galaxy.jobs.runners.AsynchronousJobRunner method) handle_tool_dependency_installation_error() (in module tool_shed.util.tool_dependency_util) handle_tool_shed_repositories() (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) handle_tool_shed_url_protocol() (in module tool_shed.util.common_util) handle_unvalidated_param_values() (galaxy.tools.Tool method) handle_unvalidated_param_values_helper() (galaxy.tools.Tool method) handle_uploaded_dataset_file() (in module galaxy.datatypes.sniff) handler_class (in module galaxy.external_services.result_handlers.basic) hapmapmart() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) has_accessible_folders() (galaxy.security.GalaxyRBACAgent method) has_accessible_library_datasets() (galaxy.security.GalaxyRBACAgent method) has_action() (galaxy.external_services.service.ActionSection method) has_adapter_base() (galaxy_utils.sequence.fastq.fastqCSSangerRead method) has_been_resubmitted() (galaxy.managers.hdas.HDAManager method) has_been_tested() (in module tool_shed.grids.util) has_data() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy_utils.sequence.fasta.fastaNamedReader method) (galaxy_utils.sequence.fastq.fastqFakeFastaScoreReader method) (galaxy_utils.sequence.fastq.fastqNamedReader method) has_dataprovider() (galaxy.datatypes.data.Data method) has_doi() (galaxy.managers.citations.BaseCitation method) (galaxy.managers.citations.DoiCitation method) has_input_for_step() (galaxy.model.WorkflowInvocation method) has_limits() (galaxy.jobs.JobWrapper method) has_manage_permissions_roles() (galaxy.model.Dataset method) (galaxy.model.LibraryDatasetDatasetAssociation method) has_metadata() (pkg_resources.FileMetadata method) (pkg_resources.IMetadataProvider method) (pkg_resources.NullProvider method) has_outputs_defined() (galaxy.model.Workflow method) has_post_authentication_actions() (galaxy.openid.providers.OpenIDProvider method) has_previous_repository_reviews() (in module tool_shed.util.review_util) has_reference_data() (galaxy.visualization.genomes.Genomes method) has_repository_dependencies (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) has_resolution (galaxy.datatypes.data.Data attribute) has_resource() (pkg_resources.IResourceProvider method) (pkg_resources.NullProvider method) has_version() (pkg_resources.Distribution method) hashcmp (pkg_resources.Distribution attribute) HasJobMetrics (class in galaxy.model) HasName (class in galaxy.model) have_shed_tool_conf_for_install() (in module tool_shed.util.shed_util_common) HDADeserializer (class in galaxy.managers.hdas) HDAFilterParser (class in galaxy.managers.hdas) HDAManager (class in galaxy.managers.hdas) HDAProvenanceController (class in galaxy.webapps.galaxy.api.provenance) HDASerializer (class in galaxy.managers.hdas) header_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.tabular.Sam method) header_startswith (galaxy_utils.sequence.vcf.VariantCall attribute) (galaxy_utils.sequence.vcf.VariantCall33 attribute) Heartbeat (class in galaxy.util.heartbeat) help (galaxy.tools.Tool attribute) help() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) help_by_page (galaxy.tools.Tool attribute) Hg (class in galaxy.webapps.tool_shed.framework.middleware.hg) HgController (class in galaxy.webapps.tool_shed.controllers.hg)

hgweb_config (galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager attribute) HgWebConfigManager (class in galaxy.webapps.tool_shed.util.hgweb_config) HiddenDataToolParameter (class in galaxy.tools.parameters.basic) HiddenField (class in galaxy.web.form_builder) HiddenToolParameter (class in galaxy.tools.parameters.basic) HideDatasetAction (class in galaxy.jobs.actions.post) HierarchicalObjectStore (class in galaxy.objectstore) HistoriesController (class in galaxy.webapps.galaxy.api.histories) History (class in galaxy.model) history() (galaxy.webapps.galaxy.controllers.root.RootController method) history_add_to() (galaxy.webapps.galaxy.controllers.root.RootController method) history_as_xml() (galaxy.webapps.galaxy.controllers.root.RootController method) history_content_type (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) history_data() (galaxy.webapps.galaxy.controllers.history.HistoryController method) history_dataset_collections() (galaxy.managers.collections.DatasetCollectionManager method) history_delete() (galaxy.webapps.galaxy.controllers.root.RootController method) history_detail() (galaxy.webapps.galaxy.controllers.mobile.Mobile method) history_get_default_permissions() (galaxy.security.GalaxyRBACAgent method) history_import() (galaxy.webapps.galaxy.controllers.root.RootController method) history_list() (galaxy.webapps.galaxy.controllers.mobile.Mobile method) history_new() (galaxy.webapps.galaxy.controllers.root.RootController method) history_options() (galaxy.webapps.galaxy.controllers.root.RootController method) history_set_default_permissions() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (galaxy.webapps.galaxy.controllers.root.RootController method) HistoryAllPublishedGrid (class in galaxy.webapps.galaxy.controllers.history) HistoryAllPublishedGrid.NameURLColumn (class in galaxy.webapps.galaxy.controllers.history) HistoryAnnotationAssociation (class in galaxy.model) HistoryAnnotationsController (class in galaxy.webapps.galaxy.api.annotations) HistoryContentAnnotationsController (class in galaxy.webapps.galaxy.api.annotations) HistoryContentsController (class in galaxy.webapps.galaxy.api.history_contents) HistoryContentTagsController (class in galaxy.webapps.galaxy.api.item_tags) HistoryController (class in galaxy.webapps.galaxy.controllers.history) HistoryDatasetAssociation (class in galaxy.model) HistoryDatasetAssociationAnnotationAssociation (class in galaxy.model) HistoryDatasetAssociationDisplayAtAuthorization (class in galaxy.model) HistoryDatasetAssociationListGrid (class in galaxy.webapps.galaxy.controllers.dataset) HistoryDatasetAssociationListGrid.HistoryColumn (class in galaxy.webapps.galaxy.controllers.dataset) HistoryDatasetAssociationListGrid.StatusColumn (class in galaxy.webapps.galaxy.controllers.dataset) HistoryDatasetAssociationRatingAssociation (class in galaxy.model) HistoryDatasetAssociationSelectionGrid (class in galaxy.webapps.galaxy.controllers.page) HistoryDatasetAssociationSubset (class in galaxy.model) HistoryDatasetAssociationTagAssociation (class in galaxy.model) HistoryDatasetCollectionAnnotationAssociation (class in galaxy.model) HistoryDatasetCollectionAssociation (class in galaxy.model) HistoryDatasetCollectionRatingAssociation (class in galaxy.model) HistoryDatasetCollectionTagAssociation (class in galaxy.model) HistoryDatasetExtendMetadataController (class in galaxy.webapps.galaxy.api.extended_metadata) HistoryDeserializer (class in galaxy.managers.histories) HistoryField (class in galaxy.web.form_builder) HistoryFilters (class in galaxy.managers.histories) HistoryListGrid (class in galaxy.webapps.galaxy.controllers.history) HistoryListGrid.DatasetsByStateColumn (class in galaxy.webapps.galaxy.controllers.history) HistoryListGrid.DeletedColumn (class in galaxy.webapps.galaxy.controllers.history) HistoryListGrid.HistoryListNameColumn (class in galaxy.webapps.galaxy.controllers.history) HistoryManager (class in galaxy.managers.histories) HistoryRatingAssociation (class in galaxy.model) HistorySelectionGrid (class in galaxy.webapps.galaxy.controllers.page) HistorySerializer (class in galaxy.managers.histories) HistoryTagAssociation (class in galaxy.model) HistoryTagsController (class in galaxy.webapps.galaxy.api.item_tags) HistoryUserShareAssociation (class in galaxy.model) hmac_new() (in module galaxy.util.hash_util) homepage_url (galaxy.webapps.tool_shed.model.Repository attribute) HostAgent (class in galaxy.security) Html (class in galaxy.datatypes.images) html_table (galaxy.datatypes.genetics.RexpBase attribute) http_error_default() (galaxy.eggs.URLRetriever method) HttpDataTransferFactory (class in galaxy.sample_tracking.data_transfer) humanize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method)

I

id (galaxy.webapps.tool_shed.model.APIKeys attribute) (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.Component attribute) (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.GalaxySession attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryCategoryAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.SkipToolTest attribute) (galaxy.webapps.tool_shed.model.Tag attribute) (galaxy.webapps.tool_shed.model.User attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) id_seq_qual_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.tabular.Sam method) iff() (in module galaxy.web.framework.helpers) Im (class in galaxy.datatypes.images) Image (class in galaxy.datatypes.images) image_type() (in module galaxy.datatypes.util.image_util) IMetadataProvider (class in pkg_resources) immediate_actions (galaxy.jobs.actions.post.ActionBox attribute) imp() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) impersonate() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) impl (galaxy.model.custom_types.JSONType attribute) (galaxy.model.custom_types.TrimmedString attribute) (galaxy.model.custom_types.UUIDType attribute) ImplicitlyConvertedDatasetAssociation (class in galaxy.model) ImplicitlyCreatedDatasetCollectionInput (class in galaxy.model) import_archive() (galaxy.webapps.galaxy.controllers.history.HistoryController method) import_capsule() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) import_datasets_to_histories() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) import_module() (in module galaxy.util.backports.importlib) import_new_workflow_deprecated() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) import_shared_workflow_deprecated() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) import_visualization() (galaxy.web.base.controller.UsesVisualizationMixin method) import_workflow() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) (in module tool_shed.util.workflow_util) import_workflows() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) ImportHistoryTool (class in galaxy.tools) ImportHistoryToolAction (class in galaxy.tools.actions.history_imp_exp) ImportsHistoryMixin (class in galaxy.web.base.controller) in_directory() (in module galaxy.util) in_ready_state() (galaxy.model.Dataset method) InappropriateDatasetContentError includes_datatypes (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) includes_tool_dependencies (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) includes_tools (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) includes_tools_for_display_in_tool_panel (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) includes_workflows (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) InconsistentDatabase increase_running_job_count() (galaxy.jobs.handler.JobHandlerQueue method) index() (galaxy.web.base.controllers.admin.Admin method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method) (galaxy.webapps.galaxy.api.configuration.ConfigurationController method) (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method) (galaxy.webapps.galaxy.api.datatypes.DatatypesController method) (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController method) (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method) (galaxy.webapps.galaxy.api.folders.FoldersController method) (galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController method) (galaxy.webapps.galaxy.api.genomes.GenomesController method) (galaxy.webapps.galaxy.api.group_roles.GroupRolesAPIController method) (galaxy.webapps.galaxy.api.group_users.GroupUsersAPIController method) (galaxy.webapps.galaxy.api.groups.GroupAPIController method) (galaxy.webapps.galaxy.api.histories.HistoriesController method) (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method) (galaxy.webapps.galaxy.api.job_files.JobFilesAPIController method) (galaxy.webapps.galaxy.api.jobs.JobController method) (galaxy.webapps.galaxy.api.libraries.LibrariesController method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.page_revisions.PageRevisionsController method) (galaxy.webapps.galaxy.api.pages.PagesController method) (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method) (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method) (galaxy.webapps.galaxy.api.request_types.RequestTypeAPIController method) (galaxy.webapps.galaxy.api.requests.RequestsAPIController method) (galaxy.webapps.galaxy.api.roles.RoleAPIController method) (galaxy.webapps.galaxy.api.samples.SamplesAPIController method) (galaxy.webapps.galaxy.api.tool_data.ToolData method) (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) (galaxy.webapps.galaxy.controllers.async.ASync method) (galaxy.webapps.galaxy.controllers.error.Error method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.library.Library method) (galaxy.webapps.galaxy.controllers.mobile.Mobile method) (galaxy.webapps.galaxy.controllers.requests.Requests method) (galaxy.webapps.galaxy.controllers.requests_admin.RequestsAdmin method) (galaxy.webapps.galaxy.controllers.root.RootController method) (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) (galaxy.webapps.galaxy.controllers.ucsc_proxy.UCSCProxy method) (galaxy.webapps.galaxy.controllers.user.User method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) (galaxy.webapps.reports.controllers.root.Report method) (galaxy.webapps.reports.controllers.system.System method) (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method) (galaxy.webapps.tool_shed.api.repository_revisions.RepositoryRevisionsController method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) index_invocations() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) IndividualTagsColumn (class in galaxy.web.framework.helpers.grids) Inflector (class in galaxy.util.inflection) info (galaxy.model.LibraryDataset attribute) info_text (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) inheritable (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) init() (in module galaxy.model.mapping) (in module galaxy.webapps.tool_shed.model.mapping) init_meta() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Newick method) (galaxy.datatypes.data.Nexus method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.tabular.Pileup method) (galaxy.model.DatasetInstance method) initial_changeset_revision (galaxy.webapps.tool_shed.model.SkipToolTest attribute) initiate_data_transfer() (galaxy.webapps.galaxy.controllers.requests_admin.RequestsAdmin method) initiate_repository_installation() (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) initiate_tool_dependency_installation() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) inject() (galaxy.workflow.modules.WorkflowModuleInjector method) inprogress_dataset_files (galaxy.model.Sample attribute) input_paths() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) InputDataCollectionModule (class in galaxy.workflow.modules) InputDataModule (class in galaxy.workflow.modules) InputModule (class in galaxy.workflow.modules) inputs() (galaxy.webapps.galaxy.api.jobs.JobController method) InRangeValidator (class in galaxy.tools.parameters.validation) insert() (galaxy.model.custom_types.MutationList method) (galaxy.util.odict.odict method) insert_on() (pkg_resources.Distribution method) InsertColumnToolOutputActionOptionFilter (class in galaxy.tools.parameters.output) install() (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) install_and_build_package() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) install_and_build_package_via_fabric() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) install_latest_repository_revision() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) install_matched_repository_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) install_model (galaxy.managers.context.ProvidesAppContext attribute) install_package() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) install_repositories() (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) install_repositories_by_revision() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) install_repository_revision() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) install_repository_revisions() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) install_specified_tool_dependencies() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) install_tool_dependencies_with_update() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) install_tool_shed_repository() (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) install_via_fabric() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) installed_len_files (galaxy.webapps.galaxy.controllers.user.User attribute) installed_repository_grid (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed attribute) installed_tool_dependencies (galaxy.tools.Tool attribute) InstalledRepositoryGrid (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.DeletedColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.DescriptionColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.NameColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.OwnerColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.RevisionColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.StatusColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.ToolShedColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.ToolShedStatusColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstallMatchedRepositoryGrid (class in tool_shed.grids.repository_grids) InstallRepositoryManager (class in tool_shed.galaxy_install.install_manager) InstallToolDependencyManager (class in tool_shed.galaxy_install.install_manager) insufficient_quality_length() (galaxy_utils.sequence.fastq.fastqCSSangerRead method) (galaxy_utils.sequence.fastq.fastqSequencingRead method)

InsufficientPermissionsException int() (galaxy.managers.base.ModelValidator method) int_range() (galaxy.managers.base.ModelValidator method) IntegerColumn (class in galaxy.web.framework.helpers.grids) IntegerToolParameter (class in galaxy.tools.parameters.basic) integrated_datatypes_configs (galaxy.datatypes.registry.Registry attribute) InternalServerError InterruptedUpload Interval (class in galaxy.datatypes.interval) interval_dataprovider() (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) interval_dict_dataprovider() (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) invalid_id_redirect() (in module galaxy.webapps.galaxy.controllers.requests_common) invalid_marker() (in module pkg_resources) invalidate_external_metadata() (galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper method) (galaxy.jobs.JobWrapper method) invocation_step() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) invoke() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) IResourceProvider (class in pkg_resources) is_accessible() (galaxy.managers.hdas.HDAManager method) is_admin_user() (galaxy.config.Configuration method) (galaxy.webapps.tool_shed.config.Configuration method) is_ascii_encoded() (galaxy_utils.sequence.fastq.fastqSequencingRead method) is_binary (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.genetics.RexpBase attribute) (galaxy.datatypes.ngsindex.BowtieIndex attribute) is_binary() (in module galaxy.util) is_bz2() (in module galaxy.datatypes.checkers) is_case() (galaxy.external_services.service.BooleanExternalServiceActionsGroupWhen method) (galaxy.external_services.service.ExternalServiceActionsGroupWhen method) (galaxy.external_services.service.ItemIsInstanceExternalServiceActionsGroupWhen method) (galaxy.external_services.service.ValueExternalServiceActionsGroupWhen method) (galaxy.tools.parameters.output.DatatypeIsInstanceToolOutputActionConditionalWhen method) (galaxy.tools.parameters.output.ToolOutputActionConditionalWhen method) (galaxy.tools.parameters.output.ValueToolOutputActionConditionalWhen method) is_check_time (galaxy.model.DeferredJob attribute) is_checked() (galaxy.web.form_builder.CheckboxField static method) is_collection (galaxy.model.DatasetCollectionElement attribute) is_column_based() (in module galaxy.datatypes.sniff) (in module tool_shed.util.tool_util) is_complete (galaxy.model.Request attribute) is_current_version() (galaxy.tools.data.ToolDataTable method) is_data_index_sample_file() (in module tool_shed.util.tool_util) is_DNA() (galaxy_utils.sequence.sequence.SequencingRead method) is_downloadable() (in module tool_shed.util.metadata_util) is_ext_unsniffable() (galaxy.datatypes.binary.Binary static method) is_first_mate() (galaxy_utils.sequence.fastq.fastqJoiner method) is_gzip() (in module galaxy.datatypes.checkers) is_handler() (galaxy.jobs.JobConfiguration method) is_hashable() (in module galaxy.util.hash_util) is_id() (galaxy.jobs.JobConfiguration method) is_job_resource_conditional (galaxy.tools.parameters.grouping.Conditional attribute) is_JSONified_value() (galaxy.datatypes.metadata.MetadataTempFile class method) is_malicious() (in module tool_shed.util.metadata_util) is_multi_byte() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) (in module galaxy.util) is_named_collection_part_name() (galaxy.tools.ToolOutputCollectionPart static method) is_new (galaxy.model.Request attribute) is_new() (galaxy.webapps.tool_shed.model.Repository method) is_outside_grace_period() (galaxy.webapps.galaxy.controllers.user.User method) is_owner() (galaxy.managers.hdas.HDAManager method) (galaxy.managers.histories.HistoryManager method) is_pending (galaxy.model.DatasetInstance attribute) is_preparing() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) is_public() (galaxy.managers.libraries.LibraryManager method) is_rejected (galaxy.model.Request attribute) is_repository_admin_role (galaxy.webapps.tool_shed.model.Role attribute) is_sniffable_binary() (galaxy.datatypes.binary.Binary static method) is_submitted (galaxy.model.Request attribute) is_tag() (galaxy.jobs.JobConfiguration method) is_tool_module_type() (in module galaxy.workflow.modules) is_tool_shed_client() (in module tool_shed.util.shed_util_common) is_true() (in module galaxy.web.framework.helpers) is_unsubmitted (galaxy.model.Request attribute) is_uuid() (in module galaxy.util) is_valid (galaxy.webapps.tool_shed.model.GalaxySession attribute) is_valid_format() (galaxy_utils.sequence.fastq.fastqSequencingRead method) is_valid_sequence() (galaxy_utils.sequence.fastq.fastqSequencingRead method) item_has_tag() (galaxy.managers.tags.TagManager method) item_permission_map_for_add() (galaxy.security.GalaxyRBACAgent method) item_permission_map_for_manage() (galaxy.security.GalaxyRBACAgent method) item_permission_map_for_modify() (galaxy.security.GalaxyRBACAgent method) ItemAccessibilityException ItemDeletionException ItemIsInstanceExternalServiceActionsGroupWhen (class in galaxy.external_services.service) ItemOwnershipException ItemRatingAssociation (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) items() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.util.bunch.Bunch method) (galaxy.util.odict.odict method) ItemSelectionGrid (class in galaxy.webapps.galaxy.controllers.page) ItemSelectionGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.page) ItemTagAssociation (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) ItemTagAssocInfo (class in galaxy.managers.tags) iter() (galaxy.datatypes.metadata.MetadataSpecCollection method) iter_blocks_split_by_species() (in module galaxy.tools.util.maf_utilities) iter_blocks_split_by_src() (in module galaxy.tools.util.maf_utilities) iter_components_by_src() (in module galaxy.tools.util.maf_utilities) iter_components_by_src_start() (in module galaxy.tools.util.maf_utilities) iter_entry_points() (pkg_resources.WorkingSet method) iter_fasta_alignment() (in module galaxy.tools.util.maf_utilities) iterate_file() (in module galaxy.web.framework.base) iteritems() (galaxy.util.odict.odict method) iterkeys() (galaxy.util.odict.odict method) itervalues() (galaxy.util.odict.odict method)

J

Job (class in galaxy.model) job_destination (galaxy.jobs.JobWrapper attribute) job_failed() (galaxy.tools.SetMetadataTool method) (galaxy.tools.Tool method) job_info() (galaxy.web.base.controllers.admin.Admin method) (galaxy.webapps.reports.controllers.jobs.Jobs method) job_pair_for_id() (galaxy.jobs.handler.JobHandlerQueue method) job_states (galaxy.jobs.deferred.DeferredJobQueue attribute) job_wrapper() (galaxy.jobs.handler.JobHandlerQueue method) JobConfiguration (class in galaxy.jobs) JobController (class in galaxy.webapps.galaxy.api.jobs) JobDestination (class in galaxy.jobs) JobExportHistoryArchive (class in galaxy.model) JobExportHistoryArchiveWrapper (class in galaxy.tools.imp_exp) JobExternalOutputMetadata (class in galaxy.model) JobExternalOutputMetadataWrapper (class in galaxy.datatypes.metadata) JobFilesAPIController (class in galaxy.webapps.galaxy.api.job_files) JobHandler (class in galaxy.jobs.handler) JobHandlerQueue (class in galaxy.jobs.handler) JobHandlerStopQueue (class in galaxy.jobs.handler) JobImportHistoryArchive (class in galaxy.model) JobImportHistoryArchiveWrapper (class in galaxy.tools.imp_exp) JobManager (class in galaxy.jobs.manager) JobMappingException JobMetricNumeric (class in galaxy.model) JobMetricText (class in galaxy.model)

JobNotReadyException JobParameter (class in galaxy.model) JobRunnerMapper (class in galaxy.jobs.mapper) Jobs (class in galaxy.webapps.reports.controllers.jobs) jobs() (galaxy.web.base.controllers.admin.Admin method) JobState (class in galaxy.jobs.runners) JobStateHistory (class in galaxy.model) JobToImplicitOutputDatasetCollectionAssociation (class in galaxy.model) JobToInputDatasetAssociation (class in galaxy.model) JobToInputDatasetCollectionAssociation (class in galaxy.model) JobToInputLibraryDatasetAssociation (class in galaxy.model) JobToolConfiguration (class in galaxy.jobs) JobToOutputDatasetAssociation (class in galaxy.model) JobToOutputDatasetCollectionAssociation (class in galaxy.model) JobToOutputLibraryDatasetAssociation (class in galaxy.model) JobWrapper (class in galaxy.jobs) join() (galaxy_utils.sequence.fastq.fastqJoiner method) Jpg (class in galaxy.datatypes.images) js() (in module galaxy.web.framework.helpers) js_helper() (in module galaxy.web.framework.helpers) json_fix() (in module galaxy.tools) (in module galaxy.util.json) jsonrpc_request() (in module galaxy.util.json) jsonrpc_response() (in module galaxy.util.json) JSONType (class in galaxy.model.custom_types)

K

k (galaxy.webapps.galaxy.api.samples.SamplesAPIController attribute) key (galaxy.webapps.tool_shed.model.APIKeys attribute) (galaxy_utils.sequence.transform.ColorSpaceConverter attribute) (pkg_resources.Distribution attribute)

keys() (galaxy.util.bunch.Bunch method) (galaxy.util.odict.odict method) known_outputs() (galaxy.tools.ToolOutputCollection method)

L

label (galaxy.tools.parameters.grouping.Conditional attribute) label() (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) Laj (class in galaxy.datatypes.images) last_access_date() (galaxy.webapps.reports.controllers.users.Users method) last_action (galaxy.webapps.tool_shed.model.GalaxySession attribute) last_check (galaxy.model.DeferredJob attribute) last_comment (galaxy.model.Request attribute) LastzCoverage (class in galaxy.datatypes.coverage) latest_event (galaxy.model.Request attribute) (galaxy.model.Sample attribute) latest_export (galaxy.model.History attribute) LateValidationError Lav (class in galaxy.datatypes.sequence) lazy_property (in module galaxy.web.framework.base) LazyProperty (class in galaxy.web.framework.base) ldda_edit_info() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) ldda_info() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) ldda_permissions() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) LDDAManager (class in galaxy.managers.lddas) LDDAProvenanceController (class in galaxy.webapps.galaxy.api.provenance) ldIndep (class in galaxy.datatypes.genetics) legal_values (galaxy.tools.parameters.basic.BooleanToolParameter attribute) legend (galaxy.web.framework.helpers.grids.Grid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) LengthValidator (class in galaxy.tools.parameters.validation) LibrariesController (class in galaxy.webapps.galaxy.api.libraries) Library (class in galaxy.model) (class in galaxy.webapps.galaxy.controllers.library) library_dataset_info() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) library_dataset_permissions() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) library_info() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) library_is_public() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) library_is_unrestricted() (galaxy.security.GalaxyRBACAgent method) library_item_updates() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) library_list_grid (galaxy.webapps.galaxy.controllers.library.Library attribute) (galaxy.webapps.galaxy.controllers.library_admin.LibraryAdmin attribute) library_path (galaxy.model.LibraryFolder attribute) library_permissions() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) LibraryAdmin (class in galaxy.webapps.galaxy.controllers.library_admin) LibraryCommon (class in galaxy.webapps.galaxy.controllers.library_common) LibraryContentsController (class in galaxy.webapps.galaxy.api.library_contents) LibraryDataset (class in galaxy.model) LibraryDatasetCollectionAnnotationAssociation (class in galaxy.model) LibraryDatasetCollectionAssociation (class in galaxy.model) LibraryDatasetCollectionRatingAssociation (class in galaxy.model) LibraryDatasetCollectionTagAssociation (class in galaxy.model) LibraryDatasetDatasetAssociation (class in galaxy.model) LibraryDatasetDatasetAssociationPermissions (class in galaxy.model) LibraryDatasetDatasetInfoAssociation (class in galaxy.model) LibraryDatasetExtendMetadataController (class in galaxy.webapps.galaxy.api.extended_metadata) LibraryDatasetPermissions (class in galaxy.model) LibraryDatasetsController (class in galaxy.webapps.galaxy.api.lda_datasets) LibraryDatasetToolParameter (class in galaxy.tools.parameters.basic) LibraryField (class in galaxy.web.form_builder) LibraryFolder (class in galaxy.model) LibraryFolderInfoAssociation (class in galaxy.model) LibraryFolderPermissions (class in galaxy.model) LibraryInfoAssociation (class in galaxy.model) LibraryListGrid (class in galaxy.webapps.galaxy.controllers.library) (class in galaxy.webapps.galaxy.controllers.library_admin) LibraryListGrid.DescriptionColumn (class in galaxy.webapps.galaxy.controllers.library) (class in galaxy.webapps.galaxy.controllers.library_admin) LibraryListGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.library) (class in galaxy.webapps.galaxy.controllers.library_admin)

LibraryListGrid.StatusColumn (class in galaxy.webapps.galaxy.controllers.library_admin) LibraryManager (class in galaxy.managers.libraries) LibraryPermissions (class in galaxy.model) line_class (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.tabular.Pileup attribute) line_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.tabular.Sam method) line_enumerator() (in module galaxy.tools.util.maf_utilities) LineCount (class in galaxy.datatypes.data) lines() (galaxy.datatypes.util.gff_util.GFFFeature method) list() (galaxy.managers.base.ModelManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.library.Library method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) list_as_xml() (galaxy.webapps.galaxy.controllers.history.HistoryController method) list_datasets_for_selection() (galaxy.webapps.galaxy.controllers.page.PageController method) list_for_run() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) list_grid() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) list_histories_for_selection() (galaxy.webapps.galaxy.controllers.page.PageController method) list_pages_for_selection() (galaxy.webapps.galaxy.controllers.page.PageController method) list_published() (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) list_shared() (galaxy.webapps.galaxy.controllers.history.HistoryController method) list_visualizations_for_selection() (galaxy.webapps.galaxy.controllers.page.PageController method) list_workflows_for_selection() (galaxy.webapps.galaxy.controllers.page.PageController method) listify() (in module galaxy.util) ListParameter (class in galaxy.datatypes.metadata) load() (galaxy.util.aliaspickler.AliasPickleModule method) (galaxy.webapps.galaxy.api.lda_datasets.LibraryDatasetsController method) (pkg_resources.EntryPoint method) load_all() (galaxy.sample_tracking.external_service_types.ExternalServiceTypesCollection method) load_build_sites() (galaxy.datatypes.registry.Registry method) load_data_transfer_settings() (galaxy.model.ExternalService method) load_datatype_converters() (galaxy.datatypes.registry.Registry method) load_datatype_sniffers() (galaxy.datatypes.registry.Registry method) load_datatypes() (galaxy.datatypes.registry.Registry method) load_dialect_impl() (galaxy.model.custom_types.JSONType method) (galaxy.model.custom_types.UUIDType method) load_display_applications() (galaxy.datatypes.registry.Registry method) load_egg_for_url() (in module galaxy.model.orm) load_entry_point() (in module pkg_resources) (pkg_resources.Distribution method) load_external_metadata_tool() (galaxy.datatypes.registry.Registry method) load_external_service_type() (galaxy.sample_tracking.external_service_types.ExternalServiceTypesCollection method) load_from_config_file() (galaxy.tools.data.ToolDataTableManager method) load_history_imp_exp_tools() (in module galaxy.tools.imp_exp) load_invalid_tool() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) load_module_sections() (in module galaxy.workflow.modules) load_sub_elems() (galaxy.external_services.service.ExternalServiceActionsGroup method) load_workflow() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) loader (pkg_resources.NullProvider attribute) loads() (galaxy.util.aliaspickler.AliasPickleModule method) (in module galaxy.util.json) local_extra_dirs() (in module galaxy.objectstore) LocalJobRunner (class in galaxy.jobs.runners.local) log_action() (galaxy.managers.context.ProvidesAppContext method) log_event() (galaxy.jobs.deferred.FakeTrans method) (galaxy.managers.context.ProvidesAppContext method) log_tempfile (module) log_user_action_async() (galaxy.webapps.galaxy.controllers.user.User method) LoggingProxy (class in galaxy.model.orm.logging_connection_proxy) login() (galaxy.webapps.galaxy.controllers.user.User method) logout() (galaxy.webapps.galaxy.controllers.user.User method) long_description (galaxy.webapps.tool_shed.model.Repository attribute) Lped (class in galaxy.datatypes.genetics) LRUCache (class in galaxy.util.lrucache) lucene_search() (in module galaxy.webapps.galaxy.controllers.library_common) LwrJobRunner (class in galaxy.jobs.runners.lwr)

M

Maf (class in galaxy.datatypes.sequence) maf_index_by_uid() (in module galaxy.tools.util.maf_utilities) MafCustomTrack (class in galaxy.datatypes.sequence) main() (in module galaxy.datatypes.converters.bgzip) (in module galaxy.datatypes.converters.fastq_to_fqtoc) (in module galaxy.datatypes.converters.gff_to_interval_index_converter) (in module galaxy.datatypes.converters.interval_to_coverage) (in module galaxy.datatypes.converters.interval_to_fli) (in module galaxy.datatypes.converters.interval_to_interval_index_converter) (in module galaxy.datatypes.converters.interval_to_tabix_converter) (in module galaxy.datatypes.converters.lped_to_fped_converter) (in module galaxy.datatypes.converters.lped_to_pbed_converter) (in module galaxy.datatypes.converters.pbed_ldreduced_converter) (in module galaxy.datatypes.converters.pbed_to_lped_converter) (in module galaxy.datatypes.converters.vcf_to_interval_index_converter) (in module galaxy.datatypes.converters.vcf_to_vcf_bgzip) (in module galaxy.datatypes.converters.wiggle_to_array_tree_converter) (in module galaxy.datatypes.converters.wiggle_to_simple_converter) (in module galaxy.tools.imp_exp.export_history) make_backup() (galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager method) make_body_iterable() (galaxy.web.framework.base.WebApplication method) make_copy() (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) make_dataset_public() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) make_dict_copy() (galaxy.datatypes.metadata.MetadataCollection method) make_file() (galaxy.web.framework.base.FieldStorage method) make_filter() (in module galaxy.web.framework.middleware.translogger) make_folder_public() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) make_html_peek_header() (galaxy.datatypes.tabular.Tabular method) make_html_peek_rows() (galaxy.datatypes.tabular.Tabular method) make_html_table() (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.tabular.Eland method) (galaxy.datatypes.tabular.Tabular method) make_library_item_public() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) make_library_public() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) make_library_uploaded_dataset() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) make_public() (galaxy.managers.libraries.LibraryManager method) make_static() (in module galaxy.web.framework.middleware.static) makeLDreduced() (in module galaxy.datatypes.converters.pbed_ldreduced_converter) makeNode() (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method) MalformedId malicious (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) MAlist (class in galaxy.datatypes.genetics) manage_addresses() (galaxy.webapps.galaxy.controllers.user.User method) manage_categories() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) manage_category_grid (galaxy.webapps.tool_shed.controllers.admin.AdminController attribute) manage_components() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_datasets() (galaxy.webapps.galaxy.controllers.requests_admin.RequestsAdmin method) manage_email_alerts() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) manage_repositories() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) manage_repositories_ready_for_review() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_repositories_reviewed_by_me() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_repositories_with_invalid_tests() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_repositories_with_reviews() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_repositories_without_reviews() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) manage_repository_admins() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) manage_repository_reviews() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_repository_reviews_of_revision() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_repository_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) manage_role_associations() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) manage_roles_and_groups_for_user() (galaxy.web.base.controllers.admin.Admin method) manage_template_inheritance() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) manage_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) manage_user_info() (galaxy.webapps.galaxy.controllers.user.User method) manage_users_and_groups_for_quota() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) manage_users_and_groups_for_role() (galaxy.web.base.controllers.admin.Admin method) manage_users_and_roles_for_group() (galaxy.web.base.controllers.admin.Admin method) ManageCategoryGrid (class in tool_shed.grids.admin_grids) ManualDataTransferPlugin (class in galaxy.jobs.deferred.manual_data_transfer) map_library_datasets_to_lddas() (in module galaxy.webapps.galaxy.controllers.library_common) map_wrap() (in module galaxy.objectstore.s3_multipart_upload) mapping() (galaxy.webapps.galaxy.api.datatypes.DatatypesController method) MAPPING_PRESET (galaxy.tools.parameters.sanitize.ToolParameterSanitizer attribute) mark_as_failed() (galaxy.jobs.runners.AsynchronousJobRunner method) mark_as_finished() (galaxy.jobs.runners.AsynchronousJobRunner method) mark_as_populated() (galaxy.model.DatasetCollection method) mark_as_queued() (galaxy.jobs.runners.BaseJobRunner method) mark_as_resubmitted() (galaxy.jobs.JobWrapper method) (galaxy.jobs.runners.BaseJobRunner method) mark_category_deleted() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) mark_deleted() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) (galaxy.model.Job method) mark_group_deleted() (galaxy.web.base.controllers.admin.Admin method) mark_quota_deleted() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) mark_role_deleted() (galaxy.web.base.controllers.admin.Admin method) mark_tool_dependency_installed() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) mark_undeleted() (galaxy.model.DatasetInstance method) mark_unhidden() (galaxy.model.DatasetInstance method) mark_user_deleted() (galaxy.web.base.controllers.admin.Admin method) marshal() (galaxy.datatypes.metadata.FileParameter class method) (galaxy.datatypes.metadata.MetadataParameter class method) (galaxy.datatypes.metadata.PythonObjectParameter class method) (galaxy.datatypes.metadata.RangeParameter class method) (galaxy.datatypes.metadata.SelectParameter class method) mask_password_from_url() (in module galaxy.util) match_collections() (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) match_datasets() (galaxy.tools.parameters.basic.DataToolParameter method) match_multirun_collections() (galaxy.tools.parameters.basic.DataCollectionToolParameter method) matched_repository_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) MatchedRepositoryGrid (class in tool_shed.grids.repository_grids) MatchedRepositoryGrid.DescriptionColumn (class in tool_shed.grids.repository_grids) MatchedRepositoryGrid.NameColumn (class in tool_shed.grids.repository_grids) MatchedRepositoryGrid.RevisionColumn (class in tool_shed.grids.repository_grids) MatchedRepositoryGrid.UserColumn (class in tool_shed.grids.repository_grids) matches_any() (galaxy.datatypes.data.Data method) MAX_LINES_RETURNED (galaxy.visualization.data_providers.basic.ColumnDataProvider attribute)

max_optional_metadata_filesize (galaxy.datatypes.data.Data attribute) MAX_PRINT_ERROR_BYTES (galaxy_utils.sequence.fastq.fastqVerboseErrorReader attribute) MAX_SEQUENCE_SIZE (galaxy.tools.util.maf_utilities.RegionAlignment attribute) md5() (in module galaxy.web.framework.helpers) MEMEXml (class in galaxy.datatypes.xml) merge() (galaxy.datatypes.data.Data static method) (galaxy.datatypes.tabular.Sam static method) (galaxy.datatypes.xml.GenericXml static method) merge_sorted_iterables() (in module galaxy.util) merge_tool_data_table() (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.data.ToolDataTable method) MessageException metadata (galaxy.model.DatasetInstance attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) metadata_isdir() (pkg_resources.IMetadataProvider method) (pkg_resources.NullProvider method) metadata_listdir() (pkg_resources.IMetadataProvider method) (pkg_resources.NullProvider method) metadata_revisions (galaxy.webapps.tool_shed.model.Repository attribute) metadata_spec (galaxy.datatypes.assembly.Amos attribute) (galaxy.datatypes.assembly.Roadmaps attribute) (galaxy.datatypes.assembly.Sequences attribute) (galaxy.datatypes.assembly.Velvet attribute) (galaxy.datatypes.binary.Ab1 attribute) (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.Bcf attribute) (galaxy.datatypes.binary.BigBed attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.binary.Binary attribute) (galaxy.datatypes.binary.CompressedArchive attribute) (galaxy.datatypes.binary.GeminiSQLite attribute) (galaxy.datatypes.binary.GenericAsn1Binary attribute) (galaxy.datatypes.binary.H5 attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.binary.Scf attribute) (galaxy.datatypes.binary.Sff attribute) (galaxy.datatypes.binary.Sra attribute) (galaxy.datatypes.binary.TwoBit attribute) (galaxy.datatypes.binary.Xlsx attribute) (galaxy.datatypes.chrominfo.ChromInfo attribute) (galaxy.datatypes.coverage.LastzCoverage attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.data.GenericAsn1 attribute) (galaxy.datatypes.data.LineCount attribute) (galaxy.datatypes.data.Newick attribute) (galaxy.datatypes.data.Nexus attribute) (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.genetics.Affybatch attribute) (galaxy.datatypes.genetics.Eigenstratgeno attribute) (galaxy.datatypes.genetics.Eigenstratpca attribute) (galaxy.datatypes.genetics.Eset attribute) (galaxy.datatypes.genetics.Fped attribute) (galaxy.datatypes.genetics.Fphe attribute) (galaxy.datatypes.genetics.GenomeGraphs attribute) (galaxy.datatypes.genetics.Lped attribute) (galaxy.datatypes.genetics.MAlist attribute) (galaxy.datatypes.genetics.Pbed attribute) (galaxy.datatypes.genetics.Phe attribute) (galaxy.datatypes.genetics.Pheno attribute) (galaxy.datatypes.genetics.Pphe attribute) (galaxy.datatypes.genetics.RexpBase attribute) (galaxy.datatypes.genetics.Rgenetics attribute) (galaxy.datatypes.genetics.SNPMatrix attribute) (galaxy.datatypes.genetics.Snptest attribute) (galaxy.datatypes.genetics.ldIndep attribute) (galaxy.datatypes.genetics.rgFeatureList attribute) (galaxy.datatypes.genetics.rgSampleList attribute) (galaxy.datatypes.genetics.rgTabList attribute) (galaxy.datatypes.images.Bmp attribute) (galaxy.datatypes.images.Eps attribute) (galaxy.datatypes.images.Gif attribute) (galaxy.datatypes.images.Gmaj attribute) (galaxy.datatypes.images.Html attribute) (galaxy.datatypes.images.Im attribute) (galaxy.datatypes.images.Image attribute) (galaxy.datatypes.images.Jpg attribute) (galaxy.datatypes.images.Laj attribute) (galaxy.datatypes.images.Pbm attribute) (galaxy.datatypes.images.Pcd attribute) (galaxy.datatypes.images.Pcx attribute) (galaxy.datatypes.images.Pdf attribute) (galaxy.datatypes.images.Pgm attribute) (galaxy.datatypes.images.Png attribute) (galaxy.datatypes.images.Ppm attribute) (galaxy.datatypes.images.Psd attribute) (galaxy.datatypes.images.Rast attribute) (galaxy.datatypes.images.Rgb attribute) (galaxy.datatypes.images.Tiff attribute) (galaxy.datatypes.images.Xbm attribute) (galaxy.datatypes.images.Xpm attribute) (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.Bed12 attribute) (galaxy.datatypes.interval.Bed6 attribute) (galaxy.datatypes.interval.BedGraph attribute) (galaxy.datatypes.interval.BedStrict attribute) (galaxy.datatypes.interval.ChromatinInteractions attribute) (galaxy.datatypes.interval.CustomTrack attribute) (galaxy.datatypes.interval.ENCODEPeak attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Gff3 attribute) (galaxy.datatypes.interval.Gtf attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.ngsindex.BowtieBaseIndex attribute) (galaxy.datatypes.ngsindex.BowtieColorIndex attribute) (galaxy.datatypes.ngsindex.BowtieIndex attribute) (galaxy.datatypes.qualityscore.QualityScore attribute) (galaxy.datatypes.qualityscore.QualityScore454 attribute) (galaxy.datatypes.qualityscore.QualityScoreIllumina attribute) (galaxy.datatypes.qualityscore.QualityScoreSOLiD attribute) (galaxy.datatypes.qualityscore.QualityScoreSolexa attribute) (galaxy.datatypes.sequence.Alignment attribute) (galaxy.datatypes.sequence.Axt attribute) (galaxy.datatypes.sequence.Fasta attribute) (galaxy.datatypes.sequence.Fastq attribute) (galaxy.datatypes.sequence.FastqCSSanger attribute) (galaxy.datatypes.sequence.FastqIllumina attribute) (galaxy.datatypes.sequence.FastqSanger attribute) (galaxy.datatypes.sequence.FastqSolexa attribute) (galaxy.datatypes.sequence.Lav attribute) (galaxy.datatypes.sequence.Maf attribute) (galaxy.datatypes.sequence.MafCustomTrack attribute) (galaxy.datatypes.sequence.RNADotPlotMatrix attribute) (galaxy.datatypes.sequence.Sequence attribute) (galaxy.datatypes.sequence.SequenceSplitLocations attribute) (galaxy.datatypes.sequence.csFasta attribute) (galaxy.datatypes.tabular.Eland attribute) (galaxy.datatypes.tabular.ElandMulti attribute) (galaxy.datatypes.tabular.FeatureLocationIndex attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.tabular.Tabular attribute) (galaxy.datatypes.tabular.Taxonomy attribute) (galaxy.datatypes.tabular.Vcf attribute) (galaxy.datatypes.tracks.GeneTrack attribute) (galaxy.datatypes.xml.CisML attribute) (galaxy.datatypes.xml.GenericXml attribute) (galaxy.datatypes.xml.MEMEXml attribute) (galaxy.datatypes.xml.Owl attribute) (galaxy.datatypes.xml.Phyloxml attribute) MetadataCollection (class in galaxy.datatypes.metadata) MetadataElement (in module galaxy.datatypes.metadata) MetadataElementSpec (class in galaxy.datatypes.metadata) MetadataFile (class in galaxy.model) MetadataInDataTableColumnValidator (class in galaxy.tools.parameters.validation) MetadataInFileColumnValidator (class in galaxy.tools.parameters.validation) MetadataParameter (class in galaxy.datatypes.metadata) MetadataSpecCollection (class in galaxy.datatypes.metadata) MetadataTempFile (class in galaxy.datatypes.metadata) MetadataToolOutputAction (class in galaxy.tools.parameters.output) MetadataType (class in galaxy.model.custom_types) MetadataValidator (class in galaxy.tools.parameters.validation) MetadataValueFilter (class in galaxy.tools.parameters.output) metrics (galaxy.model.HasJobMetrics attribute) MetricsController (class in galaxy.webapps.galaxy.api.metrics) migrate_to_current_version() (in module galaxy.model.migrate.check) (in module galaxy.webapps.tool_shed.model.migrate.check) (in module tool_shed.galaxy_install.migrate.check) MigrateToolsApplication (class in tool_shed.galaxy_install.migrate.common) mime_type() (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper method) (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper method) mimeparse (module) missing_meta() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) (galaxy.util.none_like.NoneDataset method) missing_test_components (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) missing_tools (galaxy.managers.workflows.CreatedWorkflow attribute) MissingToolException MissingToolsException (class in galaxy.managers.workflows) mkstemp() (log_tempfile.TempFile method) mkstemp_ln() (in module galaxy.util) Mobile (class in galaxy.webapps.galaxy.controllers.mobile) model (galaxy.managers.context.ProvidesAppContext attribute) model_class (galaxy.managers.base.ModelFilterParser attribute) (galaxy.managers.base.ModelManager attribute) (galaxy.managers.hdas.HDAFilterParser attribute) (galaxy.managers.hdas.HDAManager attribute) (galaxy.managers.histories.HistoryFilters attribute) (galaxy.managers.histories.HistoryManager attribute) (galaxy.managers.roles.RoleManager attribute) (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid attribute) (galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.library.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.HistoryDatasetAssociationSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.HistorySelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.VisualizationSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.WorkflowSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid attribute) (galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid attribute) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid attribute) (galaxy.webapps.galaxy.controllers.user.UserOpenIDGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) model_manager_class (galaxy.managers.base.ModelDeserializer attribute) (galaxy.managers.hdas.HDADeserializer attribute) (galaxy.managers.histories.HistoryDeserializer attribute) ModelDeserializer (class in galaxy.managers.base) ModelDeserializingError ModelFilterParser (class in galaxy.managers.base) ModelManager (class in galaxy.managers.base) ModelSerializer (class in galaxy.managers.base) ModelSerializingError ModelValidator (class in galaxy.managers.base) module_path (pkg_resources.EmptyProvider attribute) modulize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) monitor() (galaxy.jobs.handler.JobHandlerStopQueue method) (galaxy.jobs.runners.AsynchronousJobRunner method) monitor_job() (galaxy.jobs.runners.AsynchronousJobRunner method) monitor_repository_installation() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) monitor_step() (galaxy.jobs.handler.JobHandlerStopQueue method) most_recent() (galaxy.managers.histories.HistoryManager method) move_library_item() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) move_merge() (in module galaxy.util) mp_from_ids() (in module galaxy.objectstore.s3_multipart_upload) multi_select_email_alerts() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) MulticolFilterColumn (class in galaxy.web.framework.helpers.grids) multimap() (in module galaxy.objectstore.s3_multipart_upload) multipart_upload() (in module galaxy.objectstore.s3_multipart_upload) MultipleSplitterFilter (class in galaxy.tools.parameters.dynamic_options) (class in galaxy.tools.parameters.output) MutationDict (class in galaxy.model.custom_types) MutationList (class in galaxy.model.custom_types) MutationObj (class in galaxy.model.custom_types) my_writable_repositories_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) my_writable_repositories_missing_tool_test_components_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) my_writable_repositories_with_failing_tool_tests_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) my_writable_repositories_with_invalid_tools_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) my_writable_repositories_with_no_failing_tool_tests_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) my_writable_repositories_with_skip_tests_checked_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) my_writable_repositories_with_test_install_errors_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) MyWritableRepositoriesGrid (class in tool_shed.grids.repository_grids) MyWritableRepositoriesMissingToolTestComponentsGrid (class in tool_shed.grids.repository_grids) MyWritableRepositoriesWithFailingToolTestsGrid (class in tool_shed.grids.repository_grids) MyWritableRepositoriesWithInvalidToolsGrid (class in tool_shed.grids.repository_grids) MyWritableRepositoriesWithNoFailingToolTestsGrid (class in tool_shed.grids.repository_grids) MyWritableRepositoriesWithSkipTestsCheckedGrid (class in tool_shed.grids.repository_grids) MyWritableRepositoriesWithTestInstallErrorsGrid (class in tool_shed.grids.repository_grids)

N

name (galaxy.jobs.actions.post.ChangeDatatypeAction attribute) (galaxy.jobs.actions.post.ColumnSetAction attribute) (galaxy.jobs.actions.post.DefaultJobAction attribute) (galaxy.jobs.actions.post.DeleteDatasetAction attribute) (galaxy.jobs.actions.post.DeleteIntermediatesAction attribute) (galaxy.jobs.actions.post.EmailAction attribute) (galaxy.jobs.actions.post.HideDatasetAction attribute) (galaxy.jobs.actions.post.RenameDatasetAction attribute) (galaxy.jobs.actions.post.SetMetadataAction attribute) (galaxy.jobs.actions.post.TagDatasetAction attribute) (galaxy.model.LibraryDataset attribute) (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.Component attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.Tag attribute) (galaxy.workflow.modules.InputDataCollectionModule attribute) (galaxy.workflow.modules.InputDataModule attribute) (galaxy.workflow.modules.PauseModule attribute) name() (galaxy.datatypes.util.gff_util.GFFFeature method) name_autocomplete_data() (galaxy.web.base.controllers.admin.Admin method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) NameColumn (class in galaxy.webapps.galaxy.controllers.history) NamedTemporaryFile() (log_tempfile.TempFile method) NestedObjectStore (class in galaxy.objectstore) NEVER_SANITIZE (galaxy.util.Params attribute) new() (galaxy.forms.forms.FormDefinitionAddressFieldFactory method) (galaxy.forms.forms.FormDefinitionFactory method) (galaxy.forms.forms.FormDefinitionFieldFactory method) (galaxy.forms.forms.FormDefinitionHistoryFieldFactory method) (galaxy.forms.forms.FormDefinitionPasswordFieldFactory method) (galaxy.forms.forms.FormDefinitionSelectFieldFactory method) (galaxy.forms.forms.FormDefinitionTextFieldFactory method) (galaxy.forms.forms.FormDefinitionWorkflowFieldFactory method) (galaxy.forms.forms.FormDefinitionWorkflowMappingFieldFactory method) (galaxy.jobs.transfer_manager.TransferManager method) (galaxy.sample_tracking.request_types.RequestTypeFactory method) (galaxy.sample_tracking.sample.SampleStateFactory method) (galaxy.workflow.modules.SimpleWorkflowModule class method) (galaxy.workflow.modules.ToolModule class method) (galaxy.workflow.modules.WorkflowModule class method) (galaxy.workflow.modules.WorkflowModuleFactory method) new_address() (galaxy.webapps.galaxy.controllers.user.User method) new_file() (galaxy.datatypes.metadata.FileParameter method) new_file_path() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) new_provider_from_identifier() (galaxy.openid.providers.OpenIDProviders method) new_repo_alert (galaxy.webapps.tool_shed.model.User attribute) new_secure_hash() (in module galaxy.util.hash_util) new_state() (galaxy.tools.Tool method) (in module tool_shed.util.tool_util) new_upload() (in module galaxy.tools.actions.upload_common) Newick (class in galaxy.datatypes.data) Newick_Parser (class in galaxy.visualization.data_providers.phyloviz.newickparser) next() (galaxy.datatypes.util.gff_util.GFFReaderWrapper method) (galaxy.tools.exception_handling.UCSCOutWrapper method) (galaxy_utils.sequence.fasta.fastaReader method) (galaxy_utils.sequence.fastq.fastqReader method) (galaxy_utils.sequence.fastq.fastqVerboseErrorReader method) (galaxy_utils.sequence.vcf.Reader method) next_installable_changeset_revision() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) Nexus (class in galaxy.datatypes.data) Nexus_Parser (class in galaxy.visualization.data_providers.phyloviz.nexusparser) nice_size() (in module galaxy.util) (in module galaxy.webapps.reports.controllers.system) nice_total_disk_usage (galaxy.model.User attribute) (galaxy.webapps.tool_shed.model.User attribute)

NO_PROVIDER_ID (galaxy.openid.providers.OpenIDProviders attribute) NoConverterException Node (class in galaxy.visualization.data_providers.phyloviz.baseparser) NON_DATA_CONNECTION (galaxy.model.WorkflowStepConnection attribute) non_data_connection (galaxy.model.WorkflowStepConnection attribute) non_private_roles (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) non_ready_states (galaxy.model.Dataset attribute) NoneDataset (class in galaxy.util.none_like) NoopHandler (class in galaxy.jobs.manager) NoopQueue (class in galaxy.jobs) NoOptionsValidator (class in galaxy.tools.parameters.validation) NoQuotaAgent (class in galaxy.quota) normalize_path() (in module pkg_resources) normalize_runtime_state() (galaxy.workflow.modules.SimpleWorkflowModule method) (galaxy.workflow.modules.ToolModule method) not_implemented() (galaxy.web.base.controller.BaseAPIController method) NotImplemented nottest() (in module galaxy.tools.test) now() (in module galaxy.model.mapping) (in module galaxy.webapps.tool_shed.model.mapping) nullable_basestring() (galaxy.managers.base.ModelValidator method) NullDependencyManager (class in galaxy.tools.deps) NullProvider (class in pkg_resources) NullToolOutputActionOption (class in galaxy.tools.parameters.output) num_page_links (galaxy.web.framework.helpers.grids.Grid attribute) num_rows_per_page (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid attribute) (galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.library.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid attribute) (galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid attribute) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute)

O

object_store (galaxy.model.Dataset attribute) object_to_string() (in module galaxy.util) ObjectAttributeInvalidException ObjectAttributeMissingException ObjectInvalid ObjectNotFound ObjectStore (class in galaxy.objectstore) ObjectStorePopulator (class in galaxy.tools.actions) obtain() (pkg_resources.Environment method) odict (class in galaxy.util.odict) oidlog() (in module galaxy.web.framework.openid_manager) ok_to_display() (galaxy.security.GalaxyRBACAgent method) on_text_for_names() (in module galaxy.tools.actions) one() (galaxy.managers.base.ModelManager method) open_folder() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.galaxy.controllers.requests_admin.RequestsAdmin method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) open_or_build_maf_index() (in module galaxy.tools.util.maf_utilities) open_repository_files_folder() (in module tool_shed.util.shed_util_common) openid_associate() (galaxy.webapps.galaxy.controllers.user.User method) openid_auth() (galaxy.webapps.galaxy.controllers.user.User method) openid_disassociate() (galaxy.webapps.galaxy.controllers.user.User method)

openid_manage() (galaxy.webapps.galaxy.controllers.user.User method) openid_process() (galaxy.webapps.galaxy.controllers.user.User method) OpenIDManager (class in galaxy.web.framework.openid_manager) OpenIDProvider (class in galaxy.openid.providers) OpenIDProviders (class in galaxy.openid.providers) operation (galaxy.webapps.galaxy.controllers.requests.UserRequestsGrid attribute) (galaxy.webapps.galaxy.controllers.requests_admin.AdminRequestsGrid attribute) operations (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid attribute) (galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid attribute) (galaxy.webapps.galaxy.controllers.requests.UserRequestsGrid attribute) (galaxy.webapps.galaxy.controllers.requests_admin.AdminRequestsGrid attribute) (galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid attribute) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid attribute) (galaxy.webapps.galaxy.controllers.user.UserOpenIDGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid attribute) (tool_shed.grids.admin_grids.AdminRepositoryGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.DockerImageGrid attribute) (tool_shed.grids.repository_grids.EmailAlertsRepositoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithNoFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithSkipTestsCheckedGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithTestInstallErrorsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid attribute) (tool_shed.grids.repository_grids.RepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithNoFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithSkipTestsCheckedGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithTestInstallErrorsGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_grids.ValidRepositoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesReadyForReviewGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithNoToolTestsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithoutReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) (tool_shed.grids.repository_review_grids.ReviewedRepositoriesIOwnGrid attribute) option_type (in module galaxy.tools.parameters.output) optionxform() (galaxy.eggs.CaseSensitiveConfigParser method) order_components_for_installation() (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) ordinalize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) orient_block_by_region() (in module galaxy.tools.util.maf_utilities) orm_filter_parsers (galaxy.managers.base.ModelFilterParser attribute) output_paths() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) OutputParameterJSONTool (class in galaxy.tools) outputs() (galaxy.webapps.galaxy.api.jobs.JobController method) Owl (class in galaxy.datatypes.xml) OwnerAnnotationColumn (class in galaxy.web.framework.helpers.grids) OwnerColumn (class in galaxy.web.framework.helpers.grids)

P

package_tool() (galaxy.web.base.controllers.admin.Admin method) Page (class in galaxy.model) PageAllPublishedGrid (class in galaxy.webapps.galaxy.controllers.page) PageAnnotationAssociation (class in galaxy.model) PageController (class in galaxy.webapps.galaxy.controllers.page) PageListGrid (class in galaxy.webapps.galaxy.controllers.page) PageListGrid.URLColumn (class in galaxy.webapps.galaxy.controllers.page) PageRatingAssociation (class in galaxy.model) PageRevision (class in galaxy.model) PageRevisionsController (class in galaxy.webapps.galaxy.api.page_revisions) PagesController (class in galaxy.webapps.galaxy.api.pages) PageSelectionGrid (class in galaxy.webapps.galaxy.controllers.page) PageTagAssociation (class in galaxy.model) PageUserShareAssociation (class in galaxy.model) panel_entry_per_tool() (in module tool_shed.util.tool_util) ParallelismInfo (class in galaxy.jobs) param_names() (galaxy.tools.test.ParamContext method) (galaxy.tools.test.RootParamContext method) ParamContext (class in galaxy.tools.test) Params (class in galaxy.util) params_from_strings() (galaxy.tools.Tool method) (in module galaxy.tools.parameters) params_to_incoming() (in module galaxy.tools.parameters) params_to_strings() (galaxy.tools.Tool method) (in module galaxy.tools.parameters) params_with_missing_data_table_entry (galaxy.tools.Tool attribute) params_with_missing_index_file (galaxy.tools.Tool attribute) ParamsWithSpecs (class in galaxy.util) ParamValueFilter (class in galaxy.tools.parameters.dynamic_options) ParamValueToolOutputActionOptionFilter (class in galaxy.tools.parameters.output) parent (galaxy.datatypes.metadata.MetadataCollection attribute) parent_id (galaxy.webapps.tool_shed.model.Tag attribute) parent_library (galaxy.model.LibraryFolder attribute) parse() (galaxy.eggs.Crate method) (galaxy.eggs.dist.DistScrambleCrate method) (galaxy.eggs.scramble.ScrambleCrate method) (galaxy.sample_tracking.data_transfer.DataTransferFactory method) (galaxy.sample_tracking.data_transfer.FtpDataTransferFactory method) (galaxy.sample_tracking.data_transfer.HttpDataTransferFactory method) (galaxy.sample_tracking.data_transfer.ScpDataTransferFactory method) (galaxy.sample_tracking.external_service_types.ExternalServiceType method) (galaxy.tools.SetParamAction static method) (galaxy.tools.Tool method) (galaxy.tools.TracksterConfig static method) (pkg_resources.EntryPoint class method) (pkg_resources.Requirement static method) parse_bool() (galaxy.managers.base.ModelFilterParser method) parse_cast_attribute() (in module galaxy.tools.parameters.output) parse_citation() (galaxy.managers.citations.CitationsManager method) (in module galaxy.managers.citations) parse_cols_arg() (in module galaxy.tools.util.galaxyops) parse_column_definitions() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) parse_column_spec() (galaxy.tools.data.TabularToolDataTable method) parse_compare_type() (in module galaxy.tools.parameters.output) parse_data_transfer_settings() (galaxy.sample_tracking.external_service_types.ExternalServiceType method) parse_destination_params() (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) parse_egg_section() (galaxy.eggs.Crate method) (galaxy.eggs.dist.DistScrambleCrate method) (galaxy.eggs.scramble.ScrambleCrate method) parse_file_fields() (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.parameters.dynamic_options.DynamicOptions method) parse_filter() (galaxy.managers.base.ModelFilterParser method) parse_filter_params() (galaxy.web.base.controller.BaseController method) parse_filters() (galaxy.managers.base.ModelFilterParser method) parse_gff_attributes() (in module galaxy.datatypes.util.gff_util) parse_group() (pkg_resources.EntryPoint class method) parse_help() (galaxy.tools.Tool method) parse_id_list() (galaxy.managers.base.ModelFilterParser method) parse_input_elem() (galaxy.tools.Tool method) parse_input_page() (galaxy.tools.Tool method) parse_inputs() (galaxy.tools.DataSourceTool method) (galaxy.tools.Tool method) parse_limit_offset() (galaxy.web.base.controller.BaseController method) parse_map() (pkg_resources.EntryPoint class method) parse_media_range() (in module mimeparse) parse_mime_type() (in module mimeparse) parse_name() (galaxy.tools.parameters.basic.ToolParameter class method) parse_outputs() (galaxy.tools.Tool method) parse_package_elem() (in module tool_shed.util.tool_dependency_util) parse_param_elem() (galaxy.tools.Tool method) parse_redirect_url() (galaxy.tools.Tool method) parse_repository_dependency_tuple() (in module tool_shed.util.common_util) parse_requirements() (in module pkg_resources) parse_row() (galaxy.datatypes.util.gff_util.GFFIntervalToBEDReaderWrapper method) (galaxy.datatypes.util.gff_util.GFFReaderWrapper method) parse_run_details() (galaxy.sample_tracking.external_service_types.ExternalServiceType method) parse_run_details_results() (galaxy.sample_tracking.external_service_types.ExternalServiceType method) parse_species_option() (in module galaxy.tools.util.maf_utilities) parse_stdio() (galaxy.tools.Tool method) parse_tags() (galaxy.managers.tags.TagManager method) parse_tests() (in module galaxy.tools.test) parse_version() (in module pkg_resources) parse_xml() (in module galaxy.util) parse_xml_string() (in module galaxy.util) parsed_version (pkg_resources.Distribution attribute) parseData() (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method) parseFile() (galaxy.visualization.data_providers.phyloviz.baseparser.Base_Parser method) (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method) (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) (galaxy.visualization.data_providers.phyloviz.phyloxmlparser.Phyloxml_Parser method) parseNexus() (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) parseNode() (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method) (galaxy.visualization.data_providers.phyloviz.phyloxmlparser.Phyloxml_Parser method) pass_through_operations (galaxy.web.framework.helpers.grids.Grid attribute) password (galaxy.webapps.tool_shed.model.User attribute) password_manager_for_url() (tool_shed.tool_shed_registry.Registry method) PasswordField (class in galaxy.web.form_builder) PasswordResetToken (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) path (galaxy.eggs.dist.DistScrambleEgg attribute) (galaxy.eggs.Egg attribute) (galaxy.web.framework.base.Request attribute) PathMetadata (class in pkg_resources) pause() (galaxy.jobs.JobWrapper method) PauseModule (class in galaxy.workflow.modules) Pbed (class in galaxy.datatypes.genetics) Pbm (class in galaxy.datatypes.images) Pcd (class in galaxy.datatypes.images) Pcx (class in galaxy.datatypes.images) Pdf (class in galaxy.datatypes.images) peek() (galaxy.webapps.galaxy.controllers.root.RootController method) per_month_all() (galaxy.webapps.reports.controllers.jobs.Jobs method) (galaxy.webapps.reports.controllers.sample_tracking.SampleTracking method) (galaxy.webapps.reports.controllers.workflows.Workflows method) per_month_in_error() (galaxy.webapps.reports.controllers.jobs.Jobs method) per_tool() (galaxy.webapps.reports.controllers.jobs.Jobs method) per_user() (galaxy.webapps.reports.controllers.jobs.Jobs method) (galaxy.webapps.reports.controllers.sample_tracking.SampleTracking method) (galaxy.webapps.reports.controllers.workflows.Workflows method) perform_action() (galaxy.external_services.actions.ExternalServiceAction method) (galaxy.external_services.actions.ExternalServiceTemplateAction method) (galaxy.external_services.actions.ExternalServiceWebAPIAction method) (galaxy.external_services.actions.PopulatedExternalServiceAction method)

perform_action_by_name() (galaxy.external_services.service.PopulatedExternalService method) permitted_actions (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.Library attribute) (galaxy.model.RequestType attribute) (galaxy.security.RBACAgent attribute) (galaxy.webapps.tool_shed.security.RBACAgent attribute) persist_session() (galaxy.web.framework.openid_manager.OpenIDManager method) persist_uploads() (in module galaxy.tools.actions.upload_common) Pgm (class in galaxy.datatypes.images) Phe (class in galaxy.datatypes.genetics) Pheno (class in galaxy.datatypes.genetics) PhyloTree (class in galaxy.visualization.data_providers.phyloviz.baseparser) PhylovizDataProvider (class in galaxy.visualization.data_providers.phyloviz) Phyloxml (class in galaxy.datatypes.xml) Phyloxml_Parser (class in galaxy.visualization.data_providers.phyloviz.phyloxmlparser) pick_a_cycle() (galaxy.util.topsort.CycleError method) Pileup (class in galaxy.datatypes.tabular) PKG_INFO (pkg_resources.Distribution attribute) pkg_resources (module) pluralize() (galaxy.util.inflection.English method) (galaxy.util.inflection.Inflector method) Png (class in galaxy.datatypes.images) poll_active_workflow_ids() (galaxy.model.WorkflowInvocation static method) pop() (galaxy.model.custom_types.MutationList method) popitem() (galaxy.util.odict.odict method) populate() (galaxy.external_services.service.ExternalServiceActionsGroup method) (galaxy.external_services.service.PopulatedExternalService method) populate_action() (galaxy.external_services.actions.ExternalServiceAction method) populate_actions() (galaxy.model.ExternalService method) populate_external_services() (galaxy.model.Sample method) populate_module_and_state() (in module galaxy.workflow.modules) populate_state() (galaxy.tools.Tool method) populate_tool_shed_info() (galaxy.tools.Tool method) populate_widgets_from_kwd() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) populated (galaxy.model.DatasetCollection attribute) populated_states (galaxy.model.DatasetCollection attribute) PopulatedDisplayApplicationLink (class in galaxy.datatypes.display_applications.application) PopulatedExternalService (class in galaxy.external_services.service) PopulatedExternalServiceAction (class in galaxy.external_services.actions) post_authentication() (galaxy.openid.providers.OpenIDProvider method) PostJobAction (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) PostJobActionAssociation (class in galaxy.model) postprocess() (pkg_resources.ResourceManager method) Pphe (class in galaxy.datatypes.genetics) Ppm (class in galaxy.datatypes.images) prepare() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) prepare_actions() (galaxy.external_services.service.ExternalServiceActionsGroup method) prepare_activation_link() (galaxy.webapps.galaxy.controllers.user.User method) prepare_display() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) prepare_for_install() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) prepare_job() (galaxy.jobs.runners.BaseJobRunner method) preparing (galaxy.model.JobExportHistoryArchive attribute) preparing_display() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) preserve_state (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid attribute) (galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.library.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid attribute) (galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) pretty_print_json() (in module galaxy.util) pretty_print_time_interval() (in module galaxy.util) pretty_print_xml() (in module galaxy.util) pretty_stack() (in module galaxy.model.orm.logging_connection_proxy) prev_session_id (galaxy.webapps.tool_shed.model.GalaxySession attribute) preview_tools_in_changeset() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) previous_changeset_revisions() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) primary_field (galaxy.web.form_builder.SwitchingSelectField attribute) primary_file_name (galaxy.datatypes.data.Data attribute) print_nonsleeping() (galaxy.util.heartbeat.Heartbeat method) private (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.Repository attribute) private_component_reviews (galaxy.webapps.tool_shed.model.RepositoryReview attribute) private_id (galaxy.model.Role attribute) (galaxy.webapps.tool_shed.model.Role attribute) privately_share_dataset() (galaxy.security.GalaxyRBACAgent method) proceed_login() (galaxy.webapps.galaxy.controllers.user.User method) process() (galaxy.datatypes.metadata.Statement class method) process_bind_param() (galaxy.model.custom_types.JSONType method) (galaxy.model.custom_types.TrimmedString method) (galaxy.model.custom_types.UUIDType method) process_data() (galaxy.visualization.data_providers.basic.BaseDataProvider method) process_result_value() (galaxy.model.custom_types.JSONType method) (galaxy.model.custom_types.MetadataType method) (galaxy.model.custom_types.UUIDType method) process_split_file() (galaxy.datatypes.sequence.Fastq static method) produces_collections (galaxy.tools.Tool attribute) ProfileMiddleware (class in galaxy.web.framework.middleware.profile) protocol (galaxy.web.framework.base.Request attribute) provenance_item_class (galaxy.webapps.galaxy.api.provenance.HDAProvenanceController attribute) (galaxy.webapps.galaxy.api.provenance.LDDAProvenanceController attribute) provenance_item_id (galaxy.webapps.galaxy.api.provenance.HDAProvenanceController attribute) (galaxy.webapps.galaxy.api.provenance.LDDAProvenanceController attribute) ProvidesAppContext (class in galaxy.managers.context) ProvidesHistoryContext (class in galaxy.managers.context) ProvidesUserContext (class in galaxy.managers.context) pruneLD() (in module galaxy.datatypes.converters.pbed_ldreduced_converter) Psd (class in galaxy.datatypes.images) pstats_as_html() (in module galaxy.web.framework.middleware.profile) psyco_full (module) public_actions (galaxy.jobs.actions.post.ActionBox attribute) PublicURLColumn (class in galaxy.web.framework.helpers.grids) published_list_grid (galaxy.webapps.galaxy.controllers.history.HistoryController attribute) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController attribute) purge() (galaxy.managers.hdas.HDAManager method) (galaxy.managers.histories.HistoryManager method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) purge_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) purge_category() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) purge_deleted_datasets() (galaxy.webapps.galaxy.controllers.history.HistoryController method) purge_group() (galaxy.web.base.controllers.admin.Admin method) purge_library() (galaxy.webapps.galaxy.controllers.library_admin.LibraryAdmin method) purge_operation (galaxy.web.base.controllers.admin.Admin attribute) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) purge_quota() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) purge_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) purge_role() (galaxy.web.base.controllers.admin.Admin method) purge_user() (galaxy.web.base.controllers.admin.Admin method) purged (galaxy.webapps.tool_shed.model.User attribute) put() (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.NoopQueue method) (galaxy.jobs.handler.JobHandlerQueue method) (galaxy.jobs.handler.JobHandlerStopQueue method) (galaxy.jobs.runners.BaseJobRunner method) put_stop() (galaxy.jobs.NoopQueue method) PythonObjectParameter (class in galaxy.datatypes.metadata)

Q

qp (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper attribute) (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper attribute) quality() (in module mimeparse) quality_max (galaxy_utils.sequence.fastq.fastqCSSangerRead attribute) (galaxy_utils.sequence.fastq.fastqIlluminaRead attribute) (galaxy_utils.sequence.fastq.fastqSangerRead attribute) (galaxy_utils.sequence.fastq.fastqSequencingRead attribute) (galaxy_utils.sequence.fastq.fastqSolexaRead attribute) quality_min (galaxy_utils.sequence.fastq.fastqCSSangerRead attribute) (galaxy_utils.sequence.fastq.fastqIlluminaRead attribute) (galaxy_utils.sequence.fastq.fastqSangerRead attribute) (galaxy_utils.sequence.fastq.fastqSequencingRead attribute) (galaxy_utils.sequence.fastq.fastqSolexaRead attribute) quality_parsed() (in module mimeparse) QualityScore (class in galaxy.datatypes.qualityscore) QualityScore454 (class in galaxy.datatypes.qualityscore) QualityScoreIllumina (class in galaxy.datatypes.qualityscore) QualityScoreSolexa (class in galaxy.datatypes.qualityscore) QualityScoreSOLiD (class in galaxy.datatypes.qualityscore) query() (galaxy.managers.base.ModelManager method) query_associated() (galaxy.managers.base.ModelManager method) queue_history_export() (galaxy.web.base.controller.ExportsHistoryMixin method) queue_history_import() (galaxy.web.base.controller.ImportsHistoryMixin method) queue_job() (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.condor.CondorJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.local.LocalJobRunner method) (galaxy.jobs.runners.lwr.LwrJobRunner method) (galaxy.jobs.runners.tasks.TaskedJobRunner method)

queued_dataset_files (galaxy.model.Sample attribute) Quota (class in galaxy.model) quota_amount() (galaxy.model.HistoryDatasetAssociation method) quota_list_grid (galaxy.web.base.controllers.admin.Admin attribute) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) QuotaAgent (class in galaxy.quota) QuotaAPIController (class in galaxy.webapps.galaxy.api.quotas) QuotaListGrid (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.AmountColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.DescriptionColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.GroupsColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.StatusColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.UsersColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaParamParser (class in galaxy.web.params) quotas() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method)

R

RangeParameter (class in galaxy.datatypes.metadata) Rast (class in galaxy.datatypes.images) rate_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) rate_item() (galaxy.model.item_attrs.UsesItemRatings method) rate_repository() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) rating (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) rating_assoc (galaxy.managers.histories.HistoryManager attribute) rating_mapping() (in module galaxy.model.mapping) ratings (galaxy.webapps.tool_shed.model.Repository attribute) raw_param_dict() (galaxy.model.Job method) RBACAgent (class in galaxy.security) (class in galaxy.webapps.tool_shed.security) read_build_sites() (in module galaxy.util) read_config() (galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager method) read_dbnames() (in module galaxy.util) read_lines() (galaxy.web.framework.base.FieldStorage method) read_unordered_gtf() (in module galaxy.datatypes.util.gff_util) Reader (class in galaxy_utils.sequence.vcf) readline() (galaxy.tools.exception_handling.UCSCOutWrapper method) (galaxy_utils.sequence.fastq.ReadlineCountFile method) ReadlineCountFile (class in galaxy_utils.sequence.fastq) ready (galaxy.model.JobExportHistoryArchive attribute) ready() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) ready_name_for_url() (in module galaxy.util) ready_states (galaxy.model.Dataset attribute) recalculate_user_disk_usage() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) reclaim_ownership() (galaxy.jobs.JobWrapper method) recover() (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.condor.CondorJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.local.LocalJobRunner method) (galaxy.jobs.runners.lwr.LwrJobRunner method) (galaxy.jobs.runners.tasks.TaskedJobRunner method) recover_mapping() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) recover_runtime_state() (galaxy.workflow.modules.SimpleWorkflowModule method) (galaxy.workflow.modules.ToolModule method) recover_state() (galaxy.workflow.modules.SimpleWorkflowModule method) (galaxy.workflow.modules.ToolModule method) recursively_stringify_dictionary_keys() (in module galaxy.util) RecursiveNone (class in galaxy.util.none_like) redirect() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) reduce_block_by_primary_genome() (in module galaxy.tools.util.maf_utilities) reference() (galaxy.visualization.genomes.Genomes method) referer (galaxy.webapps.tool_shed.model.GalaxySession attribute) regenerate_primary_file() (galaxy.datatypes.assembly.Velvet method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.Rgenetics method) (galaxy.datatypes.ngsindex.BowtieIndex method) regenerate_statistics() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) regex_line_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.tabular.Sam method) RegexValidator (class in galaxy.tools.parameters.validation) RegionAlignment (class in galaxy.tools.util.maf_utilities) register_cleanup_file_attribute() (galaxy.jobs.runners.AsynchronousJobState method) register_finder() (in module pkg_resources) register_loader_type() (in module pkg_resources) register_namespace_handler() (in module pkg_resources) register_sniffable_binary_format() (galaxy.datatypes.binary.Binary static method) register_unsniffable_binary_ext() (galaxy.datatypes.binary.Binary static method) registered_users() (galaxy.webapps.reports.controllers.users.Users method) registered_users_per_month() (galaxy.webapps.reports.controllers.users.Users method) Registry (class in galaxy.datatypes.registry) (class in tool_shed.tool_shed_registry) reindex_tool_search() (galaxy.config.ConfiguresGalaxyMixin method) reinstall_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) reject_request() (galaxy.webapps.galaxy.controllers.requests_admin.RequestsAdmin method) relativize_symlinks() (in module galaxy.util) reload() (galaxy.datatypes.display_applications.application.DisplayApplication method) (galaxy.sample_tracking.external_service_types.ExternalServiceTypesCollection method) (galaxy.webapps.galaxy.api.tool_data.ToolData method) reload_display_application() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) reload_display_applications() (galaxy.datatypes.registry.Registry method) reload_external_service_types() (galaxy.webapps.galaxy.controllers.external_service.ExternalService method) reload_from_files() (galaxy.tools.data.ToolDataTable method) reload_genomes() (galaxy.visualization.genomes.Genomes method) reload_tables() (galaxy.tools.data.ToolDataTableManager method) reload_tool() (galaxy.web.base.controllers.admin.Admin method) reload_upload_tools() (in module tool_shed.util.tool_util) remote_addr (galaxy.webapps.tool_shed.model.GalaxySession attribute) remote_host (galaxy.web.framework.base.Request attribute) (galaxy.webapps.tool_shed.model.GalaxySession attribute) remote_hostname (galaxy.web.framework.base.Request attribute) remote_port (galaxy.web.framework.base.Request attribute) remote_repository_url (galaxy.webapps.tool_shed.model.Repository attribute) RemoteUser (class in galaxy.web.framework.middleware.remoteuser) (class in galaxy.webapps.tool_shed.framework.middleware.remoteuser) remove() (galaxy.model.custom_types.MutationList method) (pkg_resources.Environment method) remove_display_app() (galaxy.datatypes.data.Data method) remove_doppelgangers() (galaxy.eggs.Egg method) remove_entry() (galaxy.tools.data.ToolDataTable method) remove_file_or_path() (in module galaxy.eggs) remove_item_tag() (galaxy.managers.tags.TagManager method) remove_port_from_tool_shed_url() (in module tool_shed.util.common_util) remove_protocol_and_port_from_tool_shed_url() (in module tool_shed.util.common_util) remove_protocol_and_user_from_clone_url() (in module tool_shed.util.common_util) remove_protocol_from_tool_shed_url() (in module tool_shed.util.common_util) remove_repository_registry_entry() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method) remove_tag_async() (galaxy.webapps.galaxy.controllers.tag.TagsController method) remove_temp_index_file() (in module galaxy.tools.util.maf_utilities) remove_tool_dependency() (in module tool_shed.util.tool_dependency_util) remove_tool_dependency_installation_directory() (in module tool_shed.util.tool_dependency_util) RemoveValueFilter (class in galaxy.tools.parameters.dynamic_options) rename() (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) rename_async() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) rename_dataset_options (galaxy.model.RequestType attribute) rename_datasets() (galaxy.webapps.galaxy.controllers.requests_admin.RequestsAdmin method) rename_group() (galaxy.web.base.controllers.admin.Admin method) rename_quota() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) rename_role() (galaxy.web.base.controllers.admin.Admin method) RenameDatasetAction (class in galaxy.jobs.actions.post) repair_methods() (galaxy.datatypes.data.Data method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.Pileup method) repair_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) repair_repository_revision() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) repair_tool_shed_repositories() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) Repeat (class in galaxy.tools.parameters.grouping) repo_path() (galaxy.webapps.tool_shed.model.Repository method) Report (class in galaxy.webapps.reports.controllers.root) report() (galaxy.util.debugging.SimpleProfiler method) report_error() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) REPORT_FORMAT (galaxy.util.debugging.SimpleProfiler attribute) ReportsWebApplication (class in galaxy.webapps.reports.buildapp) repositories (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.Role attribute) repositories_by_user_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_i_can_administer_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_i_own_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_in_category_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_missing_tool_test_components_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_ready_for_review_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) repositories_reviewed_by_me_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) repositories_with_failing_tool_tests_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_with_invalid_tools_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_with_no_failing_tool_tests_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_with_no_tool_tests_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) repositories_with_reviews_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) repositories_with_skip_tests_checked_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_with_test_install_errors_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_without_reviews_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) RepositoriesByUserGrid (class in tool_shed.grids.repository_grids) RepositoriesController (class in galaxy.webapps.tool_shed.api.repositories) RepositoriesICanAdministerGrid (class in tool_shed.grids.repository_grids) RepositoriesInCategoryGrid (class in tool_shed.grids.repository_grids) RepositoriesInstalledException RepositoriesIOwnGrid (class in tool_shed.grids.repository_grids) RepositoriesMissingToolTestComponentsGrid (class in tool_shed.grids.repository_grids) RepositoriesReadyForReviewGrid (class in tool_shed.grids.repository_review_grids) RepositoriesReviewedByMeGrid (class in tool_shed.grids.repository_review_grids) RepositoriesWithFailingToolTestsGrid (class in tool_shed.grids.repository_grids) RepositoriesWithInvalidToolsGrid (class in tool_shed.grids.repository_grids) RepositoriesWithInvalidToolsGrid.InvalidToolConfigColumn (class in tool_shed.grids.repository_grids) RepositoriesWithNoFailingToolTestsGrid (class in tool_shed.grids.repository_grids) RepositoriesWithNoToolTestsGrid (class in tool_shed.grids.repository_review_grids) RepositoriesWithoutReviewsGrid (class in tool_shed.grids.repository_review_grids) RepositoriesWithReviewsGrid (class in tool_shed.grids.repository_review_grids) RepositoriesWithReviewsGrid.ApprovedColumn (class in tool_shed.grids.repository_review_grids) RepositoriesWithReviewsGrid.RatingColumn (class in tool_shed.grids.repository_review_grids) RepositoriesWithReviewsGrid.ReviewersColumn (class in tool_shed.grids.repository_review_grids) RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn (class in tool_shed.grids.repository_review_grids) RepositoriesWithReviewsGrid.WithReviewsRevisionColumn (class in tool_shed.grids.repository_review_grids) RepositoriesWithSkipTestsCheckedGrid (class in tool_shed.grids.repository_grids) RepositoriesWithTestInstallErrorsGrid (class in tool_shed.grids.repository_grids) Repository (class in galaxy.webapps.tool_shed.model) repository (galaxy.webapps.tool_shed.model.RepositoryCategoryAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) repository_dependencies() (galaxy.webapps.tool_shed.api.repository_revisions.RepositoryRevisionsController method) repository_dependencies_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repository_grid (galaxy.webapps.tool_shed.controllers.admin.AdminController attribute) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repository_id (galaxy.webapps.tool_shed.model.RepositoryCategoryAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) repository_ids_for_setting_metadata() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method) repository_installation_grid (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed attribute) repository_installation_status_updates() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) repository_list_grid (galaxy.web.base.controllers.admin.Admin attribute) repository_metadata (galaxy.webapps.tool_shed.model.RepositoryReview attribute) repository_metadata_grid (galaxy.webapps.tool_shed.controllers.admin.AdminController attribute) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repository_metadata_id (galaxy.webapps.tool_shed.model.SkipToolTest attribute) repository_review (galaxy.webapps.tool_shed.model.ComponentReview attribute) repository_review_id (galaxy.webapps.tool_shed.model.ComponentReview attribute) repository_reviews_by_user() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) repository_reviews_by_user_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) repository_revision (galaxy.webapps.tool_shed.model.SkipToolTest attribute) repository_tag_is_valid() (galaxy.webapps.tool_shed.framework.middleware.hg.Hg method) repository_tags_are_valid() (galaxy.webapps.tool_shed.framework.middleware.hg.Hg method) repository_was_previously_installed() (in module tool_shed.util.shed_util_common) RepositoryCategoryAssociation (class in galaxy.webapps.tool_shed.model) RepositoryController (class in galaxy.webapps.tool_shed.controllers.repository) RepositoryDependenciesGrid (class in tool_shed.grids.repository_grids) RepositoryDependenciesGrid.RequiredRepositoryColumn (class in tool_shed.grids.repository_grids) RepositoryGrid (class in tool_shed.grids.repository_grids) RepositoryGrid.CategoryColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.DeprecatedColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.DescriptionColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.EmailAlertsColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.EmailColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.HeadsColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.LatestInstallableRevisionColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.MetadataRevisionColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.NameColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.RepositoryCategoryColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.TipRevisionColumn (class in tool_shed.grids.repository_grids)

RepositoryGrid.ToolsFunctionallyCorrectColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.TypeColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.UserColumn (class in tool_shed.grids.repository_grids) RepositoryInstallationGrid (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) RepositoryInstallationGrid.DescriptionColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) RepositoryInstallationGrid.NameColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) RepositoryInstallationGrid.OwnerColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) RepositoryInstallationGrid.RevisionColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) RepositoryInstallationGrid.StatusColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) RepositoryMetadata (class in galaxy.webapps.tool_shed.model) RepositoryMetadataGrid (class in tool_shed.grids.admin_grids) (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.ChangesetRevisionColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.DatatypesColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.DeletedColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.DeprecatedColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.DoNotTestColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.DownloadableColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.HasRepositoryDependenciesColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.IdColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.IncludesDatatypesColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.IncludesToolDependenciesColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.IncludesToolsColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.IncludesWorkflowsColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.MaliciousColumn (class in tool_shed.grids.admin_grids) (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.NameColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.OwnerColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.RepositoryNameColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.RepositoryOwnerColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.RepositoryTypeColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.RevisionColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.TimeLastTestedColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.ToolsColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.ToolsFunctionallyCorrectColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.WorkflowsColumn (class in tool_shed.grids.admin_grids) RepositoryRatingAssociation (class in galaxy.webapps.tool_shed.model) RepositoryReview (class in galaxy.webapps.tool_shed.model) RepositoryReviewController (class in galaxy.webapps.tool_shed.controllers.repository_review) RepositoryReviewsByUserGrid (class in tool_shed.grids.repository_review_grids) RepositoryReviewsByUserGrid.RatingColumn (class in tool_shed.grids.repository_review_grids) RepositoryReviewsByUserGrid.RepositoryDescriptionColumn (class in tool_shed.grids.repository_review_grids) RepositoryReviewsByUserGrid.RepositoryNameColumn (class in tool_shed.grids.repository_review_grids) RepositoryReviewsByUserGrid.RevisionColumn (class in tool_shed.grids.repository_review_grids) RepositoryRevisionsController (class in galaxy.webapps.tool_shed.api.repository_revisions) RepositoryRoleAssociation (class in galaxy.webapps.tool_shed.model) RepoToolModule (class in tool_shed.util.workflow_util) RepoWorkflowModuleFactory (class in tool_shed.util.workflow_util) Request (class in galaxy.model) (class in galaxy.web.framework.base) request_grid (galaxy.webapps.galaxy.controllers.requests.Requests attribute) (galaxy.webapps.galaxy.controllers.requests_admin.RequestsAdmin attribute) request_type_grid (galaxy.webapps.galaxy.controllers.request_type.RequestType attribute) request_type_permissions() (galaxy.webapps.galaxy.controllers.request_type.RequestType method) request_types() (galaxy.managers.context.ProvidesAppContext method) RequestEvent (class in galaxy.model) RequestParameterInvalidException RequestParameterMissingException Requests (class in galaxy.webapps.galaxy.controllers.requests) RequestsAdmin (class in galaxy.webapps.galaxy.controllers.requests_admin) RequestsAPIController (class in galaxy.webapps.galaxy.api.requests) RequestsCommon (class in galaxy.webapps.galaxy.controllers.requests_common) RequestsGrid (class in galaxy.webapps.galaxy.controllers.requests_common) RequestsGrid.DescriptionColumn (class in galaxy.webapps.galaxy.controllers.requests_common) RequestsGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.requests_common) RequestsGrid.SamplesColumn (class in galaxy.webapps.galaxy.controllers.requests_common) RequestsGrid.StateColumn (class in galaxy.webapps.galaxy.controllers.requests_common) RequestsGrid.TypeColumn (class in galaxy.webapps.galaxy.controllers.requests_common) RequestType (class in galaxy.model) (class in galaxy.webapps.galaxy.controllers.request_type) RequestTypeAPIController (class in galaxy.webapps.galaxy.api.request_types) RequestTypeExternalServiceAssociation (class in galaxy.model) RequestTypeFactory (class in galaxy.sample_tracking.request_types) RequestTypeGrid (class in galaxy.webapps.galaxy.controllers.request_type) RequestTypeGrid.DescriptionColumn (class in galaxy.webapps.galaxy.controllers.request_type) RequestTypeGrid.ExternalServiceColumn (class in galaxy.webapps.galaxy.controllers.request_type) RequestTypeGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.request_type) RequestTypeGrid.RequestFormColumn (class in galaxy.webapps.galaxy.controllers.request_type) RequestTypeGrid.SampleFormColumn (class in galaxy.webapps.galaxy.controllers.request_type) RequestTypePermissions (class in galaxy.model) RequestTypeRunAssociation (class in galaxy.model) require() (galaxy.eggs.Egg method) (in module galaxy.eggs) (in module pkg_resources) (pkg_resources.EntryPoint method) (pkg_resources.WorkingSet method) require_file() (in module galaxy.tools.test) required_header_fields (galaxy_utils.sequence.vcf.VariantCall attribute) (galaxy_utils.sequence.vcf.VariantCall33 attribute) required_header_length (galaxy_utils.sequence.vcf.VariantCall attribute) (galaxy_utils.sequence.vcf.VariantCall33 attribute) Requirement (class in pkg_resources) requires() (pkg_resources.Distribution method) requires_setting_metadata (galaxy.jobs.JobWrapper attribute) (galaxy.tools.SetMetadataTool attribute) (galaxy.tools.Tool attribute) requires_user_input (galaxy.external_services.parameters.ExternalServiceParameter attribute) rerun() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) reselect_tool_panel_section() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) resend_verification() (galaxy.webapps.galaxy.controllers.user.User method) resend_verification_email() (galaxy.webapps.galaxy.controllers.user.User method) reset_all_metadata() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) reset_metadata_on_installed_repositories() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) reset_metadata_on_my_writable_repositories_in_tool_shed() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) reset_metadata_on_repositories() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method) reset_metadata_on_repository() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method) reset_metadata_on_selected_installed_repositories() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) reset_metadata_on_selected_repositories_in_tool_shed() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) reset_password() (galaxy.webapps.galaxy.controllers.user.User method) reset_repository_metadata() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) reset_to_install() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) reset_user_password() (galaxy.web.base.controllers.admin.Admin method) ResolutionError resolve() (galaxy.eggs.Crate method) (galaxy.eggs.Egg method) (pkg_resources.WorkingSet method) resolve_path() (galaxy.config.Configuration method) (in module galaxy.config) (in module galaxy.webapps.reports.config) (in module galaxy.webapps.tool_shed.config) resource_exists() (pkg_resources.ResourceManager method) resource_filename() (pkg_resources.ResourceManager method) resource_isdir() (pkg_resources.IResourceProvider method) (pkg_resources.NullProvider method) (pkg_resources.ResourceManager method) resource_listdir() (pkg_resources.IResourceProvider method) (pkg_resources.NullProvider method) (pkg_resources.ResourceManager method) resource_stream() (pkg_resources.ResourceManager method) resource_string() (pkg_resources.ResourceManager method) ResourceManager (class in pkg_resources) Response (class in galaxy.web.framework.base) restore_param() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer method) restore_text() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer method) (in module galaxy.util) restrict_scores_to_valid_range() (galaxy_utils.sequence.fastq.fastqSequencingRead class method) resume_paused_jobs() (galaxy.model.History method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) retag_async() (galaxy.webapps.galaxy.controllers.tag.TagsController method) reverse() (galaxy.util.odict.odict method) (galaxy_utils.sequence.fastq.fastqCSSangerRead method) (galaxy_utils.sequence.fastq.fastqSequencingRead method) (galaxy_utils.sequence.sequence.SequencingRead method) (in module galaxy_utils.sequence.transform) reverse_complement() (galaxy_utils.sequence.sequence.SequencingRead method) ReverseSortColumn (class in galaxy.web.framework.helpers.grids) review_tool_migration_stages() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) reviewed_repositories_i_own() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) reviewed_repositories_i_own_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) ReviewedRepositoriesIOwnGrid (class in tool_shed.grids.repository_review_grids) reviewers (galaxy.webapps.tool_shed.model.Repository attribute) reviews (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) revision() (galaxy.webapps.tool_shed.model.Repository method) RexpBase (class in galaxy.datatypes.genetics) Rgb (class in galaxy.datatypes.images) rgConv() (in module galaxy.datatypes.converters.lped_to_fped_converter) (in module galaxy.datatypes.converters.lped_to_pbed_converter) (in module galaxy.datatypes.converters.pbed_to_lped_converter) Rgenetics (class in galaxy.datatypes.genetics) rgFeatureList (class in galaxy.datatypes.genetics) rgSampleList (class in galaxy.datatypes.genetics) rgTabList (class in galaxy.datatypes.genetics) RNA_complement() (in module galaxy_utils.sequence.transform) RNA_reverse_complement() (in module galaxy_utils.sequence.transform) RNADotPlotMatrix (class in galaxy.datatypes.sequence) Roadmaps (class in galaxy.datatypes.assembly) Role (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) role (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) role_id (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) role_list_grid (galaxy.web.base.controllers.admin.Admin attribute) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (galaxy.webapps.tool_shed.controllers.admin.AdminController attribute) RoleAPIController (class in galaxy.webapps.galaxy.api.roles) RoleGrid (class in tool_shed.grids.admin_grids) RoleGrid.DescriptionColumn (class in tool_shed.grids.admin_grids) RoleGrid.GroupsColumn (class in tool_shed.grids.admin_grids) RoleGrid.NameColumn (class in tool_shed.grids.admin_grids) RoleGrid.RepositoriesColumn (class in tool_shed.grids.admin_grids) RoleGrid.StatusColumn (class in tool_shed.grids.admin_grids) RoleGrid.TypeColumn (class in tool_shed.grids.admin_grids) RoleGrid.UsersColumn (class in tool_shed.grids.admin_grids) RoleListGrid (class in galaxy.webapps.galaxy.controllers.admin) RoleListGrid.DescriptionColumn (class in galaxy.webapps.galaxy.controllers.admin) RoleListGrid.GroupsColumn (class in galaxy.webapps.galaxy.controllers.admin) RoleListGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.admin) RoleListGrid.StatusColumn (class in galaxy.webapps.galaxy.controllers.admin) RoleListGrid.TypeColumn (class in galaxy.webapps.galaxy.controllers.admin) RoleListGrid.UsersColumn (class in galaxy.webapps.galaxy.controllers.admin) RoleManager (class in galaxy.managers.roles) roles (galaxy.webapps.tool_shed.model.Repository attribute) roles() (galaxy.web.base.controllers.admin.Admin method) rollback() (galaxy.model.orm.logging_connection_proxy.LoggingProxy method) Root (in module galaxy.web.base.controller) RootController (class in galaxy.webapps.galaxy.controllers.root) RootParamContext (class in galaxy.tools.test) roundify() (in module galaxy.util) rst_to_html() (in module galaxy.util) Run (class in galaxy.model) run() (galaxy.jobs.transfer_manager.TransferManager method) (galaxy.util.heartbeat.Heartbeat method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) run_details (galaxy.model.RequestType attribute) (galaxy.model.Sample attribute) run_job() (galaxy.jobs.deferred.data_transfer.DataTransfer method) run_next() (galaxy.jobs.runners.BaseJobRunner method) run_scramble_script() (galaxy.eggs.dist.DistScrambleEgg method) (galaxy.eggs.scramble.ScrambleEgg method) run_script() (pkg_resources.IMetadataProvider method) (pkg_resources.NullProvider method) (pkg_resources.WorkingSet method) runner_name (galaxy.jobs.runners.cli.ShellJobRunner attribute) (galaxy.jobs.runners.condor.CondorJobRunner attribute) (galaxy.jobs.runners.drmaa.DRMAAJobRunner attribute) (galaxy.jobs.runners.local.LocalJobRunner attribute) (galaxy.jobs.runners.lwr.LwrJobRunner attribute) (galaxy.jobs.runners.tasks.TaskedJobRunner attribute) runner_states (galaxy.jobs.runners.JobState attribute) RunnerParams (class in galaxy.jobs.runners) running (galaxy.jobs.runners.AsynchronousJobState attribute) RuntimeException RuntimeValue (class in galaxy.tools.parameters.basic)

S

sa_session (galaxy.managers.context.ProvidesAppContext attribute) (galaxy.security.GalaxyRBACAgent attribute) (galaxy.security.HostAgent attribute) (galaxy.tools.Tool attribute) (galaxy.webapps.tool_shed.security.CommunityRBACAgent attribute) (galaxy.webapps.tool_shed.util.shed_statistics.ShedCounter attribute) (tool_shed.galaxy_install.migrate.common.MigrateToolsApplication attribute) safe_dumps() (in module galaxy.util.json) safe_extra() (in module pkg_resources) safe_name() (in module pkg_resources) safe_str_cmp() (in module galaxy.util) safe_version() (in module pkg_resources) Sam (class in galaxy.datatypes.tabular) Sample (class in galaxy.model) sample_datasets_updates() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) sample_state_updates() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) SampleDataset (class in galaxy.model) SampleEvent (class in galaxy.model) SampleRunAssociation (class in galaxy.model) samples_have_common_state (galaxy.model.Request attribute) samples_with_bar_code (galaxy.model.Request attribute) samples_without_library_destinations (galaxy.model.Request attribute) SamplesAPIController (class in galaxy.webapps.galaxy.api.samples) SampleState (class in galaxy.model) SampleStateFactory (class in galaxy.sample_tracking.sample) SampleTracking (class in galaxy.webapps.reports.controllers.sample_tracking) samtools_dataprovider() (galaxy.datatypes.binary.Bam method) sanitize_for_filename() (in module galaxy.util) sanitize_html() (in module galaxy.util.sanitize_html) sanitize_lists_to_string() (in module galaxy.util) sanitize_param() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer method) (in module galaxy.util) sanitize_text() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer method) (in module galaxy.util) save() (galaxy.webapps.galaxy.controllers.page.PageController method) save_form_definition() (galaxy.webapps.galaxy.controllers.forms.Forms method) save_to_step() (galaxy.workflow.modules.SimpleWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) save_visualization() (galaxy.web.base.controller.UsesVisualizationMixin method) save_widget_field() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) save_workflow() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) (in module tool_shed.util.workflow_util) scan() (pkg_resources.Environment method) Scf (class in galaxy.datatypes.binary) score_system (galaxy_utils.sequence.fastq.fastqCSSangerRead attribute) (galaxy_utils.sequence.fastq.fastqIlluminaRead attribute) (galaxy_utils.sequence.fastq.fastqSangerRead attribute) (galaxy_utils.sequence.fastq.fastqSequencingRead attribute) (galaxy_utils.sequence.fastq.fastqSolexaRead attribute) ScpDataTransferFactory (class in galaxy.sample_tracking.data_transfer) scramble() (galaxy.eggs.scramble.ScrambleCrate method) (galaxy.eggs.scramble.ScrambleEgg method) scramble_dir (galaxy.eggs.scramble.ScrambleEgg attribute) ScrambleCrate (class in galaxy.eggs.scramble) ScrambleEgg (class in galaxy.eggs.scramble) ScrambleFailure script_dir (galaxy.eggs.scramble.ScrambleEgg attribute) search() (galaxy.tools.search.ToolBoxSearch method) (galaxy.webapps.galaxy.api.jobs.JobController method) SearchController (class in galaxy.webapps.galaxy.api.search) Section (class in galaxy.tools.parameters.grouping) secure() (galaxy.managers.folders.FolderManager method) (galaxy.managers.libraries.LibraryManager method) security_check() (galaxy.web.base.controller.SharableItemSecurityMixin method) (in module galaxy.managers.base) SecurityHelper (class in galaxy.web.security) select_datasets_to_transfer() (galaxy.webapps.galaxy.controllers.requests_admin.RequestsAdmin method) select_files_to_delete() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) select_previous_review() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) SelectField (class in galaxy.web.form_builder) SelectParameter (class in galaxy.datatypes.metadata) SelectToolParameter (class in galaxy.tools.parameters.basic) send_email_notification() (galaxy.model.Request method) send_file() (in module galaxy.web.framework.base) send_mail() (in module galaxy.util) send_redirect() (galaxy.web.framework.base.Response method) send_to_owner() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) send_verification_email() (galaxy.webapps.galaxy.controllers.user.User method) sentry_dsn_public (galaxy.config.Configuration attribute) (galaxy.webapps.tool_shed.config.Configuration attribute) sep() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SimpleComputeEnvironment method) sep2tabs() (in module galaxy.datatypes.sniff) Sequence (class in galaxy.datatypes.sequence) sequence_as_DNA() (galaxy_utils.sequence.sequence.SequencingRead method) sequence_as_RNA() (galaxy_utils.sequence.sequence.SequencingRead method) sequence_space (galaxy_utils.sequence.fastq.fastqCSSangerRead attribute) (galaxy_utils.sequence.fastq.fastqIlluminaRead attribute) (galaxy_utils.sequence.fastq.fastqSangerRead attribute) (galaxy_utils.sequence.fastq.fastqSequencingRead attribute) (galaxy_utils.sequence.fastq.fastqSolexaRead attribute) Sequences (class in galaxy.datatypes.assembly) SequenceSplitLocations (class in galaxy.datatypes.sequence) SequencingRead (class in galaxy_utils.sequence.sequence) serialize() (galaxy.managers.base.ModelSerializer method) serialize_contents() (galaxy.managers.histories.HistorySerializer method) serialize_date() (galaxy.managers.base.ModelSerializer method) serialize_display_apps() (galaxy.managers.hdas.HDASerializer method) serialize_history_state() (galaxy.managers.histories.HistorySerializer method) serialize_id() (galaxy.managers.base.ModelSerializer method) serialize_old_display_applications() (galaxy.managers.hdas.HDASerializer method) serialize_state_counts() (galaxy.managers.histories.HistorySerializer method) serialize_state_ids() (galaxy.managers.histories.HistorySerializer method) serialize_to_view() (galaxy.managers.base.ModelSerializer method) serialize_type_id() (galaxy.managers.hdas.HDASerializer method) serialize_urls() (galaxy.managers.hdas.HDASerializer method) serialize_visualization_links() (galaxy.managers.hdas.HDASerializer method) serve_ready_history_export() (galaxy.web.base.controller.ExportsHistoryMixin method) session (galaxy.web.framework.base.DefaultWebTransaction attribute) session() (galaxy.managers.base.ModelManager method) session_key (galaxy.webapps.tool_shed.model.GalaxySession attribute) set() (galaxy.tools.data.ToolDataTableManager method) set_accessible_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) set_all_dataset_permissions() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_all_library_permissions() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_allow_push() (galaxy.webapps.tool_shed.model.Repository method) set_amount() (galaxy.model.Quota method) set_as_current() (galaxy.webapps.galaxy.controllers.history.HistoryController method) set_attribute_metadata() (galaxy.datatypes.interval.Gff method) set_basic_defaults() (in module galaxy.jobs.splitters.basic) set_check_interval() (galaxy.model.DeferredJob method) set_checked() (galaxy.web.form_builder.CheckboxField method) set_collection_elements() (galaxy.managers.collections.DatasetCollectionManager method) set_command_line() (galaxy.model.Job method) (galaxy.model.Task method) set_content_type() (galaxy.web.framework.base.Response method) set_current() (galaxy.managers.histories.HistoryManager method) set_current_by_id() (galaxy.managers.histories.HistoryManager method) set_dataset_permission() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_dataset_permissions() (galaxy.security.HostAgent method) set_dataset_state() (galaxy.model.DatasetInstance method) set_datatypes_registry() (in module galaxy.model) set_dbkey() (galaxy.model.DatasetInstance method) set_default_permissions() (galaxy.webapps.galaxy.controllers.user.User method) set_default_quota() (galaxy.quota.QuotaAgent method) set_default_values() (galaxy.datatypes.registry.Registry method) set_defaults() (galaxy.jobs.runners.JobState method) set_dir() (galaxy.eggs.dist.DistScrambleEgg method) (galaxy.eggs.Egg method) set_disk_usage() (galaxy.model.GalaxySession method) (galaxy.model.User method) (galaxy.webapps.tool_shed.model.User method) set_distribution() (galaxy.eggs.Egg method) set_email_alerts() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) set_entity_group_associations() (galaxy.security.GalaxyRBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) set_entity_quota_associations() (galaxy.quota.QuotaAgent method) set_entity_role_associations() (galaxy.security.GalaxyRBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) set_entity_user_associations() (galaxy.security.GalaxyRBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) set_extra_files_path() (galaxy.model.Dataset method) set_extraction_path() (pkg_resources.ResourceManager method) set_file_name() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) set_final_state() (galaxy.model.Job method) set_from_dict() (galaxy.model.DatasetCollection method) (galaxy.model.DatasetCollectionInstance method) set_handler() (galaxy.model.Job method) set_id() (galaxy.model.Task method) set_image_paths() (in module tool_shed.util.shed_util_common) set_imported() (galaxy.model.Job method) set_info() (galaxy.model.Job method) (galaxy.model.LibraryDataset method) (galaxy.model.Task method) set_input_datasets() (galaxy.model.Job method) set_input_library_datasets() (galaxy.model.Job method) set_item() (galaxy.model.HistoryDatasetAssociationRatingAssociation method) (galaxy.model.HistoryDatasetCollectionRatingAssociation method) (galaxy.model.HistoryRatingAssociation method) (galaxy.model.ItemRatingAssociation method) (galaxy.model.LibraryDatasetCollectionRatingAssociation method) (galaxy.model.PageRatingAssociation method) (galaxy.model.StoredWorkflowRatingAssociation method) (galaxy.model.VisualizationRatingAssociation method) (galaxy.webapps.tool_shed.model.ItemRatingAssociation method) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation method) set_item_extended_metadata_obj() (galaxy.web.base.controller.UsesExtendedMetadataMixin method) set_job() (galaxy.model.Task method) set_job_destination() (galaxy.jobs.JobWrapper method) set_job_runner_external_id() (galaxy.model.Task method) set_job_runner_external_pid() (galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper method) set_last_check() (galaxy.model.DeferredJob method) set_library_dataset_dataset_association() (galaxy.model.LibraryDataset method) set_library_item_permission() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_malicious() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) set_max_optional_metadata_filesize() (galaxy.datatypes.data.Data method) set_meta() (galaxy.datatypes.assembly.Velvet method) (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.Rgenetics method) (galaxy.datatypes.interval.Bed method) (galaxy.datatypes.interval.BedStrict method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Gff3 method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) (galaxy.datatypes.qualityscore.QualityScoreSOLiD method) (galaxy.datatypes.sequence.Fastq method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.sequence.MafCustomTrack method) (galaxy.datatypes.sequence.Sequence method) (galaxy.datatypes.sequence.csFasta method) (galaxy.datatypes.tabular.Eland method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.Tabular method) (galaxy.datatypes.tabular.Vcf method) (galaxy.model.DatasetInstance method) set_metadata() (galaxy.model.DatasetInstance method) set_name() (galaxy.model.LibraryDataset method) set_non_data_connection() (galaxy.model.WorkflowStepConnection method) set_object_store_id() (galaxy.tools.actions.ObjectStorePopulator method) set_output_datasets() (galaxy.model.Job method) set_output_library_datasets() (galaxy.model.Job method) set_param_filename() (galaxy.model.Job method) set_parameters() (galaxy.model.Job method) (galaxy.model.Task method) set_params() (galaxy.model.Job method) set_parent() (galaxy.datatypes.metadata.MetadataCollection method) set_password_cleartext() (galaxy.model.User method) (galaxy.webapps.tool_shed.model.User method) set_peek() (galaxy.datatypes.binary.Ab1 method) (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.binary.BigWig method) (galaxy.datatypes.binary.Binary method) (galaxy.datatypes.binary.CompressedArchive method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.H5 method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.binary.Scf method) (galaxy.datatypes.binary.Sff method) (galaxy.datatypes.binary.Sra method) (galaxy.datatypes.binary.TwoBit method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.SNPMatrix method) (galaxy.datatypes.images.Gmaj method) (galaxy.datatypes.images.Html method) (galaxy.datatypes.images.Image method) (galaxy.datatypes.images.Laj method) (galaxy.datatypes.ngsindex.BowtieIndex method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.sequence.RNADotPlotMatrix method) (galaxy.datatypes.sequence.Sequence method) (galaxy.datatypes.sequence.SequenceSplitLocations method) (galaxy.datatypes.tabular.Tabular method) (galaxy.datatypes.xml.CisML method) (galaxy.datatypes.xml.GenericXml method) (galaxy.datatypes.xml.MEMEXml method) (galaxy.datatypes.xml.Owl method) (galaxy.datatypes.xml.Phyloxml method) (galaxy.model.DatasetInstance method) set_permission_roles() (galaxy.managers.libraries.LibraryManager method) set_permissions() (galaxy.webapps.galaxy.api.folders.FoldersController method) (galaxy.webapps.galaxy.api.libraries.LibrariesController method) set_permissions_old() (galaxy.webapps.galaxy.api.libraries.LibrariesController method) set_position() (galaxy.tools.util.maf_utilities.RegionAlignment method) set_post_job_actions() (galaxy.model.Job method) set_prepare_input_files_cmd() (galaxy.model.Task method) set_public_username() (galaxy.web.base.controller.SharableMixin method) set_quota_default() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) set_range() (galaxy.tools.util.maf_utilities.RegionAlignment method) set_raw_data() (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Text method) (galaxy.model.DatasetInstance method) set_repository_attributes() (in module tool_shed.util.shed_util_common) set_request_type_permissions() (galaxy.security.GalaxyRBACAgent method) set_runner() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) set_runner_external_id() (galaxy.model.Job method) set_runner_name() (galaxy.model.Job method)

set_session_id() (galaxy.model.Job method) set_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) (galaxy.web.form_builder.PasswordField method) (galaxy.web.form_builder.TextArea method) (galaxy.web.form_builder.TextField method) set_slug_async() (galaxy.web.base.controller.SharableMixin method) set_state() (galaxy.model.Job method) (galaxy.model.Task method) set_stderr() (galaxy.model.Task method) set_stdout() (galaxy.model.Task method) set_tags_from_list() (galaxy.managers.tags.TagManager method) (galaxy.web.base.controller.UsesTagsMixin method) set_task_runner_external_id() (galaxy.model.Task method) set_task_runner_name() (galaxy.model.Task method) set_tool_dependency_attributes() (in module tool_shed.util.tool_dependency_util) set_tool_id() (galaxy.model.Job method) set_tool_version() (galaxy.model.Job method) set_tool_versions() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) set_total_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) set_transaction_factory() (galaxy.web.framework.base.WebApplication method) set_user_id() (galaxy.model.Job method) set_user_pref_async() (galaxy.webapps.galaxy.controllers.user.User method) set_working_directory() (galaxy.model.Task method) setdefault() (galaxy.util.odict.odict method) SetMetadataAction (class in galaxy.jobs.actions.post) SetMetadataTool (class in galaxy.tools) SetMetadataToolAction (class in galaxy.tools.actions.metadata) SetParamAction (class in galaxy.tools) settings() (galaxy.webapps.galaxy.controllers.mobile.Mobile method) setup_external_metadata() (galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper method) (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) setup_job() (galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper method) SETUP_NEEDED (galaxy.web.framework.openid_manager.OpenIDManager attribute) Sff (class in galaxy.datatypes.binary) sharable_owner() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) sharable_repository() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) sharable_repository_revision() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) SharableItemSecurityMixin (class in galaxy.web.base.controller) SharableMixin (class in galaxy.web.base.controller) share() (galaxy.web.base.controller.SharableMixin method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) share_restricted() (galaxy.webapps.galaxy.controllers.history.HistoryController method) shared_list_grid (galaxy.webapps.galaxy.controllers.history.HistoryController attribute) SharedComputeEnvironment (class in galaxy.jobs) SharedHistoryListGrid (class in galaxy.webapps.galaxy.controllers.history) SharedHistoryListGrid.DatasetsByStateColumn (class in galaxy.webapps.galaxy.controllers.history) SharedHistoryListGrid.SharedByColumn (class in galaxy.webapps.galaxy.controllers.history) sharing() (galaxy.web.base.controller.SharableMixin method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) SharingStatusColumn (class in galaxy.web.framework.helpers.grids) shed_tool_data_path (galaxy.webapps.tool_shed.config.Configuration attribute) ShedCounter (class in galaxy.webapps.tool_shed.util.shed_statistics) ShellJobRunner (class in galaxy.jobs.runners.cli) show() (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method) (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method) (galaxy.webapps.galaxy.api.folders.FoldersController method) (galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController method) (galaxy.webapps.galaxy.api.genomes.GenomesController method) (galaxy.webapps.galaxy.api.group_roles.GroupRolesAPIController method) (galaxy.webapps.galaxy.api.group_users.GroupUsersAPIController method) (galaxy.webapps.galaxy.api.groups.GroupAPIController method) (galaxy.webapps.galaxy.api.histories.HistoriesController method) (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method) (galaxy.webapps.galaxy.api.jobs.JobController method) (galaxy.webapps.galaxy.api.lda_datasets.LibraryDatasetsController method) (galaxy.webapps.galaxy.api.libraries.LibrariesController method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.pages.PagesController method) (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method) (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method) (galaxy.webapps.galaxy.api.request_types.RequestTypeAPIController method) (galaxy.webapps.galaxy.api.requests.RequestsAPIController method) (galaxy.webapps.galaxy.api.roles.RoleAPIController method) (galaxy.webapps.galaxy.api.tool_data.ToolData method) (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method) (galaxy.webapps.tool_shed.api.repository_revisions.RepositoryRevisionsController method) show_editable_form_definition() (galaxy.webapps.galaxy.controllers.forms.Forms method) show_field() (galaxy.webapps.galaxy.api.tool_data.ToolData method) show_invocation() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) show_item_checkboxes (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute) (tool_shed.grids.repository_grids.DockerImageGrid attribute) show_library_item() (galaxy.security.GalaxyRBACAgent method) show_params() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) show_roles() (galaxy.webapps.galaxy.api.lda_datasets.LibraryDatasetsController method) show_version() (galaxy.webapps.galaxy.api.lda_datasets.LibraryDatasetsController method) shrink_stream_by_size() (in module galaxy.util) shrink_string_by_size() (in module galaxy.util) shutdown() (galaxy.jobs.deferred.DeferredJobQueue method) (galaxy.jobs.NoopQueue method) (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.handler.JobHandler method) (galaxy.jobs.handler.JobHandlerQueue method) (galaxy.jobs.handler.JobHandlerStopQueue method) (galaxy.jobs.manager.JobManager method) (galaxy.jobs.manager.NoopHandler method) (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.lwr.LwrJobRunner method) (galaxy.jobs.transfer_manager.TransferManager method) (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.util.heartbeat.Heartbeat method) (galaxy.webapps.reports.app.UniverseApplication method) (galaxy.webapps.tool_shed.app.UniverseApplication method) (tool_shed.galaxy_install.migrate.common.MigrateToolsApplication method) simple_mapping() (in module galaxy.model.mapping) SimpleComputeEnvironment (class in galaxy.jobs) SimpleProfiler (class in galaxy.util.debugging) SimpleWorkflowModule (class in galaxy.workflow.modules) SINGLE_CHAR_ABBR (galaxy.managers.histories.HistorySerializer attribute) SingleTagContentsParser (class in galaxy.webapps.galaxy.controllers.workflow) singularize() (galaxy.util.inflection.English method) (galaxy.util.inflection.Inflector method) sites (galaxy.security.HostAgent attribute) size() (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) size_to_bytes() (in module galaxy.util) skip() (galaxy.managers.base.ModelSerializer method) SkipAttribute skipped() (in module galaxy.tools.util.galaxyops) SkipToolTest (class in galaxy.webapps.tool_shed.model) sleep() (galaxy.jobs.deferred.Sleeper method) (galaxy.jobs.transfer_manager.Sleeper method) Sleeper (class in galaxy.jobs.deferred) (class in galaxy.jobs.transfer_manager) slice() (galaxy_utils.sequence.fastq.fastqSequencingRead method) smart_str() (in module galaxy.util) SMRTPortalPlugin (class in galaxy.jobs.deferred.pacific_biosciences_smrt_portal) sniff() (galaxy.datatypes.assembly.Amos method) (galaxy.datatypes.assembly.Roadmaps method) (galaxy.datatypes.assembly.Sequences method) (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.binary.Bcf method) (galaxy.datatypes.binary.BigWig method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.binary.Sff method) (galaxy.datatypes.binary.Sra method) (galaxy.datatypes.binary.TwoBit method) (galaxy.datatypes.binary.Xlsx method) (galaxy.datatypes.data.Newick method) (galaxy.datatypes.data.Nexus method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.SNPMatrix method) (galaxy.datatypes.genetics.rgSampleList method) (galaxy.datatypes.images.Bmp method) (galaxy.datatypes.images.Eps method) (galaxy.datatypes.images.Gif method) (galaxy.datatypes.images.Gmaj method) (galaxy.datatypes.images.Html method) (galaxy.datatypes.images.Im method) (galaxy.datatypes.images.Image method) (galaxy.datatypes.images.Jpg method) (galaxy.datatypes.images.Pbm method) (galaxy.datatypes.images.Pcd method) (galaxy.datatypes.images.Pcx method) (galaxy.datatypes.images.Pdf method) (galaxy.datatypes.images.Pgm method) (galaxy.datatypes.images.Png method) (galaxy.datatypes.images.Ppm method) (galaxy.datatypes.images.Psd method) (galaxy.datatypes.images.Rast method) (galaxy.datatypes.images.Rgb method) (galaxy.datatypes.images.Tiff method) (galaxy.datatypes.images.Xbm method) (galaxy.datatypes.images.Xpm method) (galaxy.datatypes.interval.Bed method) (galaxy.datatypes.interval.BedStrict method) (galaxy.datatypes.interval.ChromatinInteractions method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.ENCODEPeak method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Gff3 method) (galaxy.datatypes.interval.Gtf method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) (galaxy.datatypes.ngsindex.BowtieIndex method) (galaxy.datatypes.qualityscore.QualityScore454 method) (galaxy.datatypes.qualityscore.QualityScoreSOLiD method) (galaxy.datatypes.sequence.Axt method) (galaxy.datatypes.sequence.Fasta method) (galaxy.datatypes.sequence.Fastq method) (galaxy.datatypes.sequence.Lav method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.sequence.RNADotPlotMatrix method) (galaxy.datatypes.sequence.SequenceSplitLocations method) (galaxy.datatypes.sequence.csFasta method) (galaxy.datatypes.tabular.Eland method) (galaxy.datatypes.tabular.ElandMulti method) (galaxy.datatypes.tabular.Pileup method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.Vcf method) (galaxy.datatypes.xml.CisML method) (galaxy.datatypes.xml.GenericXml method) (galaxy.datatypes.xml.MEMEXml method) (galaxy.datatypes.xml.Owl method) (galaxy.datatypes.xml.Phyloxml method) sniffable_binary_formats (galaxy.datatypes.binary.Binary attribute) sniffers() (galaxy.webapps.galaxy.api.datatypes.DatatypesController method) SNPMatrix (class in galaxy.datatypes.genetics) Snptest (class in galaxy.datatypes.genetics) sort() (galaxy.web.framework.helpers.grids.BooleanColumn method) (galaxy.web.framework.helpers.grids.CommunityRatingColumn method) (galaxy.web.framework.helpers.grids.DateTimeColumn method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.framework.helpers.grids.IntegerColumn method) (galaxy.web.framework.helpers.grids.OwnerColumn method) (galaxy.web.framework.helpers.grids.ReverseSortColumn method) (galaxy.web.framework.helpers.grids.TextColumn method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid.DeletedColumn method) sort_block_components_by_block() (in module galaxy.tools.util.maf_utilities) sort_by_attr() (galaxy.security.GalaxyRBACAgent method) (in module galaxy.web.base.controller) (in module galaxy.webapps.galaxy.controllers.library_common) (in module galaxy.webapps.tool_shed.model) SortByColumnFilter (class in galaxy.tools.parameters.dynamic_options) source_dataset_chain (galaxy.model.DatasetInstance attribute) source_library_dataset (galaxy.model.DatasetInstance attribute) spec (galaxy.datatypes.metadata.MetadataCollection attribute) specified_date() (galaxy.webapps.reports.controllers.users.Users method) specified_date_handler() (galaxy.webapps.reports.controllers.jobs.Jobs method) (galaxy.webapps.reports.controllers.sample_tracking.SampleTracking method) (galaxy.webapps.reports.controllers.workflows.Workflows method) specified_date_list_grid (galaxy.webapps.reports.controllers.jobs.Jobs attribute) (galaxy.webapps.reports.controllers.sample_tracking.SampleTracking attribute) (galaxy.webapps.reports.controllers.workflows.Workflows attribute) specified_month() (galaxy.webapps.reports.controllers.users.Users method) specified_month_all() (galaxy.webapps.reports.controllers.jobs.Jobs method) specified_month_in_error() (galaxy.webapps.reports.controllers.jobs.Jobs method) SpecifiedDateListGrid (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.sample_tracking) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.CreateTimeColumn (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.sample_tracking) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.EmailColumn (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.sample_tracking) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.JobIdColumn (class in galaxy.webapps.reports.controllers.jobs) SpecifiedDateListGrid.RequestNameColumn (class in galaxy.webapps.reports.controllers.sample_tracking) SpecifiedDateListGrid.SpecifiedDateColumn (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.sample_tracking) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.StateColumn (class in galaxy.webapps.reports.controllers.jobs) SpecifiedDateListGrid.ToolColumn (class in galaxy.webapps.reports.controllers.jobs) SpecifiedDateListGrid.UserColumn (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.sample_tracking) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.WorkflowNameColumn (class in galaxy.webapps.reports.controllers.workflows) SplicedAlignment (class in galaxy.tools.util.maf_utilities) split() (galaxy.datatypes.data.Text class method) (galaxy.datatypes.sequence.Alignment method) (galaxy.datatypes.sequence.Fasta class method) (galaxy.datatypes.sequence.Fastq class method) (galaxy.datatypes.sequence.Sequence method) (galaxy_utils.sequence.fastq.fastqSplitter method) split_output_name() (galaxy.tools.ToolOutputCollectionPart static method) split_sections() (in module pkg_resources) splitLinebyWhitespaces() (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) SQlite (class in galaxy.datatypes.binary) sqlite_datadictprovider() (galaxy.datatypes.binary.SQlite method) sqlite_dataprovider() (galaxy.datatypes.binary.SQlite method) sqlite_datatableprovider() (galaxy.datatypes.binary.SQlite method) Sra (class in galaxy.datatypes.binary) src_merge() (in module galaxy.tools.util.maf_utilities) src_split() (in module galaxy.tools.util.maf_utilities) stack_trace_string() (in module galaxy.util.debugging) standard_filters (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.library.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.admin_grids.AdminRepositoryGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) start (galaxy.tools.util.maf_utilities.SplicedAlignment attribute) start() (galaxy.jobs.handler.JobHandler method) (galaxy.jobs.handler.JobHandlerQueue method) (galaxy.jobs.manager.JobManager method) (galaxy.jobs.manager.NoopHandler method) (galaxy.util.debugging.SimpleProfiler method) state (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionInstance attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.Request attribute) (galaxy.model.Sample attribute) state_fields (galaxy.workflow.modules.InputDataCollectionModule attribute) (galaxy.workflow.modules.InputDataModule attribute) (galaxy.workflow.modules.PauseModule attribute) StateColumn (class in galaxy.web.framework.helpers.grids) Statement (class in galaxy.datatypes.metadata) states (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.DeferredJob attribute) (galaxy.model.Job attribute) (galaxy.model.Request attribute) (galaxy.model.Task attribute) (galaxy.model.TransferJob attribute) (galaxy.model.WorkflowInvocation attribute) StaticValueFilter (class in galaxy.tools.parameters.dynamic_options) status_code (galaxy.exceptions.ActionInputError attribute) (galaxy.exceptions.AdminRequiredException attribute) (galaxy.exceptions.AuthenticationFailed attribute) (galaxy.exceptions.AuthenticationRequired attribute) (galaxy.exceptions.ConfigDoesNotAllowException attribute) (galaxy.exceptions.ConfigurationError attribute) (galaxy.exceptions.Conflict attribute) (galaxy.exceptions.DeprecatedMethod attribute) (galaxy.exceptions.DuplicatedIdentifierException attribute) (galaxy.exceptions.DuplicatedSlugException attribute) (galaxy.exceptions.InconsistentDatabase attribute) (galaxy.exceptions.InsufficientPermissionsException attribute) (galaxy.exceptions.InternalServerError attribute) (galaxy.exceptions.ItemAccessibilityException attribute) (galaxy.exceptions.ItemOwnershipException attribute) (galaxy.exceptions.MalformedId attribute) (galaxy.exceptions.MessageException attribute) (galaxy.exceptions.NotImplemented attribute) (galaxy.exceptions.ObjectAttributeInvalidException attribute) (galaxy.exceptions.ObjectAttributeMissingException attribute) (galaxy.exceptions.ObjectNotFound attribute) (galaxy.exceptions.RequestParameterInvalidException attribute) (galaxy.exceptions.RequestParameterMissingException attribute) (galaxy.exceptions.ToolMetaParameterException attribute) (galaxy.exceptions.UnknownContentsType attribute) status_for_installed_repository() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) stderr() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) stdout() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) step_invocations_by_step_id() (galaxy.model.WorkflowInvocation method) step_invocations_for_step_id() (galaxy.model.WorkflowInvocation method) step_states_by_step_id() (galaxy.model.WorkflowInvocation method) stop() (galaxy.jobs.handler.DefaultJobDispatcher method) stop_err() (in module galaxy.datatypes.converters.fastqsolexa_to_fasta_converter) (in module galaxy.datatypes.converters.fastqsolexa_to_qual_converter) (in module galaxy.datatypes.converters.interval_to_bed_converter) (in module galaxy.datatypes.converters.interval_to_bedstrict_converter) (in module galaxy.datatypes.converters.wiggle_to_simple_converter) stop_job() (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.condor.CondorJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.local.LocalJobRunner method) (galaxy.jobs.runners.lwr.LwrJobRunner method) (galaxy.jobs.runners.tasks.TaskedJobRunner method) STOP_SIGNAL (galaxy.jobs.handler.JobHandlerQueue attribute) (galaxy.jobs.handler.JobHandlerStopQueue attribute) store_jobtemplate() (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) stored_list_grid (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface attribute) (galaxy.webapps.galaxy.controllers.history.HistoryController attribute) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController attribute) stored_workflow (galaxy.managers.workflows.CreatedWorkflow attribute) StoredWorkflow (class in galaxy.model) StoredWorkflowAllPublishedGrid (class in galaxy.webapps.galaxy.controllers.workflow) StoredWorkflowAnnotationAssociation (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) StoredWorkflowListGrid (class in galaxy.webapps.galaxy.controllers.workflow) StoredWorkflowListGrid.StepsColumn (class in galaxy.webapps.galaxy.controllers.workflow) StoredWorkflowMenuEntry (class in galaxy.model) StoredWorkflowRatingAssociation (class in galaxy.model) StoredWorkflowTagAssociation (class in galaxy.model) StoredWorkflowUserShareAssociation (class in galaxy.model) stream() (galaxy.util.streamball.StreamBall method) (galaxy.util.streamball.ZipBall method) stream_to_file() (in module galaxy.datatypes.sniff) stream_to_open_named_file() (in module galaxy.datatypes.sniff) StreamBall (class in galaxy.util.streamball) string_as_bool() (in module galaxy.eggs) (in module galaxy.util) string_as_bool_or_none() (in module galaxy.util) string_replace() (galaxy.util.inflection.Base method) string_standard_ops() (galaxy.managers.base.ModelFilterParser method) string_to_object() (in module galaxy.util) StringFunctionFilter (class in galaxy.tools.parameters.output) stringify_dictionary_keys() (in module galaxy.util) stripwd() (in module galaxy.model.orm.logging_connection_proxy) structure() (galaxy.webapps.galaxy.controllers.history.HistoryController method) submit_request() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) subscribe() (pkg_resources.WorkingSet method) SUCCESS (galaxy.web.framework.openid_manager.OpenIDManager attribute) supported_display_apps (galaxy.datatypes.data.Data attribute) supported_field_types (galaxy.model.FormDefinition attribute) (galaxy.model.Sample attribute) switch_to_history() (galaxy.webapps.galaxy.controllers.history.HistoryController method) SwitchingSelectField (class in galaxy.web.form_builder) synchronized() (in module galaxy.util) System (class in galaxy.webapps.reports.controllers.system)

T

table (galaxy.webapps.tool_shed.model.APIKeys attribute) (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.Component attribute) (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.GalaxySession attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.PasswordResetToken attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryCategoryAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.SkipToolTest attribute) (galaxy.webapps.tool_shed.model.Tag attribute) (galaxy.webapps.tool_shed.model.User attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) tableize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) Tabular (class in galaxy.datatypes.tabular) TabularToolDataField (class in galaxy.tools.data) TabularToolDataTable (class in galaxy.tools.data) Tag (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) tag (galaxy.tools.parameters.output.BooleanFilter attribute) (galaxy.tools.parameters.output.ColumnReplaceFilter attribute) (galaxy.tools.parameters.output.ColumnStripFilter attribute) (galaxy.tools.parameters.output.DatatypeIsInstanceToolOutputActionConditionalWhen attribute) (galaxy.tools.parameters.output.FormatToolOutputAction attribute) (galaxy.tools.parameters.output.FromDataTableOutputActionOption attribute) (galaxy.tools.parameters.output.FromFileToolOutputActionOption attribute) (galaxy.tools.parameters.output.FromParamToolOutputActionOption attribute) (galaxy.tools.parameters.output.InsertColumnToolOutputActionOptionFilter attribute) (galaxy.tools.parameters.output.MetadataToolOutputAction attribute) (galaxy.tools.parameters.output.MetadataValueFilter attribute) (galaxy.tools.parameters.output.MultipleSplitterFilter attribute) (galaxy.tools.parameters.output.NullToolOutputActionOption attribute) (galaxy.tools.parameters.output.ParamValueToolOutputActionOptionFilter attribute) (galaxy.tools.parameters.output.StringFunctionFilter attribute) (galaxy.tools.parameters.output.ToolOutputAction attribute) (galaxy.tools.parameters.output.ToolOutputActionConditional attribute) (galaxy.tools.parameters.output.ToolOutputActionConditionalWhen attribute) (galaxy.tools.parameters.output.ToolOutputActionGroup attribute) (galaxy.tools.parameters.output.ToolOutputActionOption attribute) (galaxy.tools.parameters.output.ToolOutputActionOptionFilter attribute) (galaxy.tools.parameters.output.ValueToolOutputActionConditionalWhen attribute) tag_assoc (galaxy.managers.hdas.HDAManager attribute) (galaxy.managers.histories.HistoryManager attribute) tag_autocomplete_data() (galaxy.webapps.galaxy.controllers.tag.TagsController method) tag_mapping() (in module galaxy.model.mapping) tag_outputs() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) TagDatasetAction (class in galaxy.jobs.actions.post) tagged_item_class (galaxy.webapps.galaxy.api.item_tags.HistoryContentTagsController attribute) (galaxy.webapps.galaxy.api.item_tags.HistoryTagsController attribute) (galaxy.webapps.galaxy.api.item_tags.WorkflowTagsController attribute) tagged_item_id (galaxy.webapps.galaxy.api.annotations.HistoryAnnotationsController attribute) (galaxy.webapps.galaxy.api.annotations.HistoryContentAnnotationsController attribute) (galaxy.webapps.galaxy.api.annotations.WorkflowAnnotationsController attribute) (galaxy.webapps.galaxy.api.item_tags.HistoryContentTagsController attribute) (galaxy.webapps.galaxy.api.item_tags.HistoryTagsController attribute) (galaxy.webapps.galaxy.api.item_tags.WorkflowTagsController attribute) TagManager (class in galaxy.managers.tags) TagsController (class in galaxy.webapps.galaxy.controllers.tag) Task (class in galaxy.model) TaskedJobRunner (class in galaxy.jobs.runners.tasks) TaskMetricNumeric (class in galaxy.model) TaskMetricText (class in galaxy.model) TaskWrapper (class in galaxy.jobs) Taxonomy (class in galaxy.datatypes.tabular) TempFile (class in log_tempfile) TempFileHandler (class in galaxy.tools.util.maf_utilities) Template (class in galaxy.external_services.actions) template (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid attribute) (galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.library.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid attribute) (galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid attribute) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid attribute) (galaxy.webapps.galaxy.controllers.user.UserOpenIDGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) templates() (in module galaxy.web.framework.helpers) templates_dict() (galaxy.model.LibraryDatasetDatasetAssociation method) templates_json() (galaxy.model.LibraryDatasetDatasetAssociation method) terminal_states (galaxy.model.TransferJob attribute) test_data() (galaxy.tools.test.ToolTestBuilder method) test_data_iter() (in module galaxy.tools.test) test_install_error (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) tests (galaxy.tools.Tool attribute) Text (class in galaxy.datatypes.data) text_data() (galaxy.managers.hdas.HDAManager method) TextArea (class in galaxy.web.form_builder) TextColumn (class in galaxy.web.framework.helpers.grids) TextField (class in galaxy.web.form_builder) TextToolParameter (class in galaxy.tools.parameters.basic) tfoot (galaxy.web.form_builder.FTPFileField attribute) thead (galaxy.web.form_builder.FTPFileField attribute) thread_is_sleeping() (galaxy.util.heartbeat.Heartbeat method) Tiff (class in galaxy.datatypes.images) time_ago() (in module galaxy.web.framework.helpers) time_last_tested (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) timenow() (in module galaxy.datatypes.converters.lped_to_fped_converter) (in module galaxy.datatypes.converters.lped_to_pbed_converter) (in module galaxy.datatypes.converters.pbed_ldreduced_converter) (in module galaxy.datatypes.converters.pbed_to_lped_converter) times_downloaded (galaxy.webapps.tool_shed.model.Repository attribute) tip() (galaxy.webapps.tool_shed.model.Repository method) title (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid attribute) (galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.library.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.HistoryDatasetAssociationSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.HistorySelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.VisualizationSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.WorkflowSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid attribute) (galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid attribute) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid attribute) (galaxy.webapps.galaxy.controllers.user.UserOpenIDGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.DatatypesGrid attribute) (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithNoFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithSkipTestsCheckedGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithTestInstallErrorsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid attribute) (tool_shed.grids.repository_grids.RepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithNoFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithSkipTestsCheckedGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithTestInstallErrorsGrid attribute) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ToolDependenciesGrid attribute) (tool_shed.grids.repository_grids.ToolsGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_grids.ValidRepositoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesReadyForReviewGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithNoToolTestsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithoutReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) (tool_shed.grids.repository_review_grids.ReviewedRepositoriesIOwnGrid attribute) title_by_index() (galaxy.tools.parameters.grouping.UploadDataset method) title_plural (galaxy.tools.parameters.grouping.Repeat attribute) (galaxy.tools.parameters.grouping.Section attribute) (galaxy.tools.parameters.grouping.UploadDataset attribute) titleize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) tmp_dir (galaxy.datatypes.metadata.MetadataTempFile attribute) to_base_space() (galaxy_utils.sequence.transform.ColorSpaceConverter method) to_bibtex() (galaxy.managers.citations.BibtexCitation method) (galaxy.managers.citations.DoiCitation method) to_color_space() (galaxy_utils.sequence.transform.ColorSpaceConverter method) to_dict() (galaxy.managers.citations.BaseCitation method) (galaxy.model.History method) (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.HistoryDatasetCollectionAssociation method) (galaxy.model.Job method) (galaxy.model.Library method) (galaxy.model.LibraryDataset method) (galaxy.model.LibraryDatasetCollectionAssociation method) (galaxy.model.LibraryDatasetDatasetAssociation method) (galaxy.model.LibraryFolder method) (galaxy.model.Page method) (galaxy.model.PageRevision method) (galaxy.model.StoredWorkflow method) (galaxy.model.Workflow method) (galaxy.model.WorkflowInvocation method) (galaxy.model.WorkflowInvocationStep method) (galaxy.model.WorkflowRequest method) (galaxy.model.item_attrs.Dictifiable method) (galaxy.tools.Tool method) (galaxy.tools.data.TabularToolDataField method) (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.GenomeBuildParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.TextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.grouping.Conditional method) (galaxy.tools.parameters.grouping.ConditionalWhen method) (galaxy.tools.parameters.grouping.Group method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.visualization.genomes.Genome method) (galaxy.web.form_builder.SelectField method) (galaxy.webapps.tool_shed.model.Repository method) to_DNA() (in module galaxy_utils.sequence.transform) to_external_value() (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) to_filename() (in module pkg_resources) to_history_dataset_association() (galaxy.model.LibraryDatasetDatasetAssociation method) to_html_value() (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.TextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) to_JSON() (galaxy.datatypes.metadata.MetadataTempFile method) to_json() (galaxy.tools.Tool method) to_JSON_dict() (galaxy.datatypes.metadata.MetadataCollection method) to_library_dataset_dataset_association() (galaxy.model.HistoryDatasetAssociation method) to_param_dict_string() (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) to_python() (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter method) (galaxy.tools.parameters.basic.IntegerToolParameter method) (galaxy.tools.parameters.basic.LibraryDatasetToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) to_RNA() (in module galaxy_utils.sequence.transform) to_safe_string() (galaxy.datatypes.metadata.DictParameter method) (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) to_string() (galaxy.datatypes.metadata.ColumnTypesParameter method) (galaxy.datatypes.metadata.DictParameter method) (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.ListParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.datatypes.metadata.PythonObjectParameter method) (galaxy.datatypes.metadata.SelectParameter method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.LibraryDatasetToolParameter method) (galaxy.tools.parameters.basic.TextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) to_unicode() (in module galaxy.web.framework.helpers) to_xml_file() (galaxy.datatypes.registry.Registry method) (galaxy.tools.data.ToolDataTableManager method) toJson() (galaxy.visualization.data_providers.phyloviz.baseparser.Base_Parser method) (galaxy.visualization.data_providers.phyloviz.baseparser.Node method) token (galaxy.webapps.tool_shed.model.PasswordResetToken attribute) Tool (class in galaxy.tools) tool (galaxy.tools.parameters.output.ToolOutputAction attribute) (galaxy.tools.parameters.output.ToolOutputActionConditional attribute) (galaxy.tools.parameters.output.ToolOutputActionGroup attribute) (galaxy.tools.parameters.output.ToolOutputActionOption attribute) (galaxy.tools.parameters.output.ToolOutputActionOptionFilter attribute) tool_class (in module galaxy.tools) tool_dependencies_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) tool_dependency_grid (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed attribute) tool_dependency_status_updates() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) tool_directory() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) tool_fail() (in module galaxy.tools.util.maf_utilities) tool_help() (galaxy.webapps.galaxy.controllers.root.RootController method) tool_lineages() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method) tool_per_month() (galaxy.webapps.reports.controllers.jobs.Jobs method) tool_search() (galaxy.webapps.galaxy.controllers.root.RootController method) tool_shed.galaxy_install (module) tool_shed.galaxy_install.grids.admin_toolshed_grids (module) tool_shed.galaxy_install.install_manager (module) tool_shed.galaxy_install.migrate.check (module) tool_shed.galaxy_install.migrate.common (module) tool_shed.grids.admin_grids (module) tool_shed.grids.repository_grids (module)

tool_shed.grids.repository_review_grids (module) tool_shed.grids.util (module) tool_shed.tool_shed_registry (module) tool_shed.util.common_util (module) tool_shed.util.encoding_util (module) tool_shed.util.metadata_util (module) tool_shed.util.readme_util (module) tool_shed.util.review_util (module) tool_shed.util.shed_util_common (module) tool_shed.util.tool_dependency_util (module) tool_shed.util.tool_util (module) tool_shed.util.workflow_util (module) tool_shed_decode() (in module tool_shed.util.encoding_util) tool_shed_encode() (in module tool_shed.util.encoding_util) tool_shed_get() (in module tool_shed.util.common_util) tool_shed_is_this_tool_shed() (in module tool_shed.util.shed_util_common) tool_shed_repository (galaxy.tools.Tool attribute) tool_test_results (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) tool_type (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.GenomeIndexTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.SetMetadataTool attribute) (galaxy.tools.Tool attribute) tool_version (galaxy.tools.Tool attribute) tool_version_list_grid (galaxy.web.base.controllers.admin.Admin attribute) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) tool_versions (galaxy.tools.Tool attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) tool_versions() (galaxy.web.base.controllers.admin.Admin method) ToolAction (class in galaxy.tools.actions) ToolBox (class in galaxy.tools) toolbox_filters() (galaxy.webapps.galaxy.controllers.user.User method) ToolBoxSearch (class in galaxy.tools.search) ToolData (class in galaxy.webapps.galaxy.api.tool_data) ToolDataTable (class in galaxy.tools.data) ToolDataTableManager (class in galaxy.tools.data) ToolDependenciesGrid (class in tool_shed.grids.repository_grids) ToolDependenciesGrid.ToolDependencyColumn (class in tool_shed.grids.repository_grids) ToolDependencyGrid (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) ToolDependencyGrid.NameColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) ToolDependencyGrid.StatusColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) ToolDependencyGrid.TypeColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) ToolDependencyGrid.VersionColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) ToolInputTranslator (class in galaxy.tools.parameters.input_translation) ToolMetaParameterException ToolModule (class in galaxy.workflow.modules) ToolNotFoundException ToolOutput (class in galaxy.tools) ToolOutputAction (class in galaxy.tools.parameters.output) ToolOutputActionConditional (class in galaxy.tools.parameters.output) ToolOutputActionConditionalWhen (class in galaxy.tools.parameters.output) ToolOutputActionGroup (class in galaxy.tools.parameters.output) ToolOutputActionOption (class in galaxy.tools.parameters.output) ToolOutputActionOptionFilter (class in galaxy.tools.parameters.output) ToolOutputBase (class in galaxy.tools) ToolOutputCollection (class in galaxy.tools) ToolOutputCollectionPart (class in galaxy.tools) ToolOutputCollectionStructure (class in galaxy.tools) ToolParameter (class in galaxy.tools.parameters.basic) ToolParameterSanitizer (class in galaxy.tools.parameters.sanitize) ToolRunner (class in galaxy.webapps.galaxy.controllers.tool_runner) tools_by_id (galaxy.tools.ToolBox attribute) tools_functionally_correct (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) tools_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) ToolsGrid (class in tool_shed.grids.repository_grids) ToolsGrid.ToolsColumn (class in tool_shed.grids.repository_grids) ToolShedRepositoriesController (class in galaxy.webapps.galaxy.api.tool_shed_repositories) ToolTagAssociation (class in galaxy.model) ToolTestBuilder (class in galaxy.tools.test) ToolVersionListGrid (class in galaxy.webapps.galaxy.controllers.admin) ToolVersionListGrid.ToolIdColumn (class in galaxy.webapps.galaxy.controllers.admin) ToolVersionListGrid.ToolVersionsColumn (class in galaxy.webapps.galaxy.controllers.admin) topsort() (in module galaxy.util.topsort) topsort_levels() (in module galaxy.util.topsort) total_disk_usage (galaxy.model.GalaxySession attribute) (galaxy.model.User attribute) (galaxy.webapps.tool_shed.model.User attribute) trace() (galaxy.web.framework.base.WebApplication method) TraceLoggerProxy (class in galaxy.model.orm.logging_connection_proxy) track_type (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.BedGraph attribute) (galaxy.datatypes.interval.ChromatinInteractions attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Gff3 attribute) (galaxy.datatypes.interval.Gtf attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.tabular.Vcf attribute) TracksterConfig (class in galaxy.tools) transfer_error_dataset_files (galaxy.model.Sample attribute) transfer_part() (in module galaxy.objectstore.s3_multipart_upload) transfer_status (galaxy.model.SampleDataset attribute) transfer_status() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) TransferJob (class in galaxy.model) TransferManager (class in galaxy.jobs.transfer_manager) transferred_dataset_files (galaxy.model.Sample attribute) transferring_dataset_files (galaxy.model.Sample attribute) transform_publicname() (in module galaxy.security.validate_user_input) transform_scores_to_valid_range() (galaxy_utils.sequence.fastq.fastqSequencingRead class method) transform_scores_to_valid_range_ascii() (galaxy_utils.sequence.fastq.fastqSequencingRead class method) translate() (galaxy.tools.parameters.input_translation.ToolInputTranslator method) TransLogger (class in galaxy.web.framework.middleware.translogger) TrimmedString (class in galaxy.model.custom_types) trow (galaxy.web.form_builder.FTPFileField attribute) truncate() (in module galaxy.web.framework.helpers) TwoBit (class in galaxy.datatypes.binary) type (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter attribute) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter attribute) (galaxy.datatypes.display_applications.parameters.DisplayApplicationTemplateParameter attribute) (galaxy.external_services.actions.ExternalServiceAction attribute) (galaxy.external_services.actions.ExternalServiceTemplateAction attribute) (galaxy.external_services.actions.ExternalServiceWebAPIAction attribute) (galaxy.external_services.actions.ExternalServiceWebAction attribute) (galaxy.external_services.parameters.ExternalServiceParameter attribute) (galaxy.external_services.parameters.ExternalServiceTemplateParameter attribute) (galaxy.external_services.result_handlers.basic.ExternalServiceActionJQueryGridResultHandler attribute) (galaxy.external_services.result_handlers.basic.ExternalServiceActionJSONResultHandler attribute) (galaxy.external_services.result_handlers.basic.ExternalServiceActionResultHandler attribute) (galaxy.external_services.result_handlers.basic.ExternalServiceActionURLRedirectResultHandler attribute) (galaxy.external_services.service.BooleanExternalServiceActionsGroupWhen attribute) (galaxy.external_services.service.ExternalServiceActionsConditional attribute) (galaxy.external_services.service.ExternalServiceActionsGroupWhen attribute) (galaxy.external_services.service.ItemIsInstanceExternalServiceActionsGroupWhen attribute) (galaxy.external_services.service.ValueExternalServiceActionsGroupWhen attribute) (galaxy.forms.forms.FormDefinitionAddressFieldFactory attribute) (galaxy.forms.forms.FormDefinitionFieldFactory attribute) (galaxy.forms.forms.FormDefinitionHistoryFieldFactory attribute) (galaxy.forms.forms.FormDefinitionPasswordFieldFactory attribute) (galaxy.forms.forms.FormDefinitionSelectFieldFactory attribute) (galaxy.forms.forms.FormDefinitionTextFieldFactory attribute) (galaxy.forms.forms.FormDefinitionWorkflowFieldFactory attribute) (galaxy.forms.forms.FormDefinitionWorkflowMappingFieldFactory attribute) (galaxy.sample_tracking.data_transfer.DataTransferFactory attribute) (galaxy.sample_tracking.data_transfer.FtpDataTransferFactory attribute) (galaxy.sample_tracking.data_transfer.HttpDataTransferFactory attribute) (galaxy.sample_tracking.data_transfer.ScpDataTransferFactory attribute) (galaxy.tools.parameters.grouping.Conditional attribute) (galaxy.tools.parameters.grouping.Repeat attribute) (galaxy.tools.parameters.grouping.Section attribute) (galaxy.tools.parameters.grouping.UploadDataset attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.Tag attribute) (galaxy.workflow.modules.InputDataCollectionModule attribute) (galaxy.workflow.modules.InputDataModule attribute) (galaxy.workflow.modules.PauseModule attribute) (galaxy.workflow.modules.ToolModule attribute) (tool_shed.util.workflow_util.RepoToolModule attribute) type() (galaxy.managers.base.ModelValidator method) type_key (galaxy.tools.data.TabularToolDataTable attribute) types (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.Role attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.webapps.tool_shed.model.Role attribute)

U

UCI (class in galaxy.model) ucsc_links() (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) UCSCLimitException UCSCOutWrapper (class in galaxy.tools.exception_handling) UCSCProxy (class in galaxy.webapps.galaxy.controllers.ucsc_proxy) umask_fix_perms() (in module galaxy.util) unaccent() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) undeletable() (galaxy.model.DatasetInstance method) undelete() (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method) (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController method) (galaxy.webapps.galaxy.api.histories.HistoriesController method) (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) undelete_address() (galaxy.webapps.galaxy.controllers.user.User method) undelete_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) undelete_category() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) undelete_external_service() (galaxy.webapps.galaxy.controllers.external_service.ExternalService method) undelete_form_definition() (galaxy.webapps.galaxy.controllers.forms.Forms method) undelete_group() (galaxy.web.base.controllers.admin.Admin method) undelete_library() (galaxy.webapps.galaxy.controllers.library_admin.LibraryAdmin method) undelete_library_item() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) undelete_operation (galaxy.web.base.controllers.admin.Admin attribute) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) undelete_quota() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) undelete_repository() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) undelete_request() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) undelete_request_type() (galaxy.webapps.galaxy.controllers.request_type.RequestType method) undelete_role() (galaxy.web.base.controllers.admin.Admin method) undelete_user() (galaxy.web.base.controllers.admin.Admin method) underscore() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) UNDERSCORED_OPS (galaxy.managers.base.ModelFilterParser attribute) unhide() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) unhide_datasets() (galaxy.model.History method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) unicodify() (in module galaxy.util) uninstall_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) unique_id() (in module galaxy.util) UniqueValueFilter (class in galaxy.tools.parameters.dynamic_options) UniverseApplication (class in galaxy.webapps.reports.app) (class in galaxy.webapps.tool_shed.app) unknown_base (galaxy_utils.sequence.transform.ColorSpaceConverter attribute) unknown_color (galaxy_utils.sequence.transform.ColorSpaceConverter attribute) unknown_starttag() (galaxy.webapps.galaxy.controllers.workflow.SingleTagContentsParser method) UnknownContentsType UnknownExtra unpack_archive() (in module galaxy.tools.imp_exp.unpack_tar_gz_archive) unpack_if_needed() (galaxy.eggs.dist.DistScrambleEgg method) (galaxy.eggs.Egg method) unpack_source() (galaxy.eggs.scramble.ScrambleEgg method) unpack_tar() (galaxy.eggs.scramble.ScrambleEgg method) unpack_zip() (galaxy.eggs.scramble.ScrambleEgg method) unpack_zipfile() (in module galaxy.eggs) unset_item_extended_metadata_obj() (galaxy.web.base.controller.UsesExtendedMetadataMixin method) unset_quota_default() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) unsniffable_binary_formats (galaxy.datatypes.binary.Binary attribute) UnspecifiedBuildValidator (class in galaxy.tools.parameters.validation) unstructured_path_rewriter() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SimpleComputeEnvironment method) untransferred_dataset_files (galaxy.model.Sample attribute) UnvalidatedValue (class in galaxy.tools.parameters.basic) unwrap() (galaxy.datatypes.metadata.MetadataElementSpec method) (galaxy.datatypes.metadata.MetadataParameter method) up_to_date (galaxy.model.JobExportHistoryArchive attribute) update() (galaxy.managers.base.ModelManager method) (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.model.WorkflowInvocation method) (galaxy.model.WorkflowInvocationStep method) (galaxy.util.Params method) (galaxy.util.odict.odict method) (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method) (galaxy.webapps.galaxy.api.folders.FoldersController method) (galaxy.webapps.galaxy.api.group_roles.GroupRolesAPIController method) (galaxy.webapps.galaxy.api.group_users.GroupUsersAPIController method) (galaxy.webapps.galaxy.api.groups.GroupAPIController method) (galaxy.webapps.galaxy.api.histories.HistoriesController method) (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method) (galaxy.webapps.galaxy.api.libraries.LibrariesController method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method) (galaxy.webapps.galaxy.api.requests.RequestsAPIController method) (galaxy.webapps.galaxy.api.samples.SamplesAPIController method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method) (galaxy.webapps.tool_shed.api.repository_revisions.RepositoryRevisionsController method) update_external_service_form_definition() (galaxy.webapps.galaxy.controllers.external_service.ExternalService method) update_from_file() (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) update_invocation_step() (galaxy.managers.workflows.WorkflowsManager method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) update_permissions() (galaxy.webapps.galaxy.api.lda_datasets.LibraryDatasetsController method) update_request_state() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) update_runtime_state() (galaxy.workflow.modules.SimpleWorkflowModule method) update_sample_dataset_status() (galaxy.webapps.galaxy.controllers.requests_admin.RequestsAdmin method) update_sample_state() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) update_state() (galaxy.tools.Tool method) (galaxy.workflow.modules.SimpleWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) update_time (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.GalaxySession attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.SkipToolTest attribute) (galaxy.webapps.tool_shed.model.User attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) update_to_changeset_revision() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) update_tool_shed_repository_status() (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) update_tool_shed_status_for_installed_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) update_type_values (galaxy.webapps.galaxy.api.samples.SamplesAPIController attribute) update_types (galaxy.webapps.galaxy.api.samples.SamplesAPIController attribute) update_workflow_from_dict() (galaxy.managers.workflows.WorkflowContentsManager method) updated_changeset_revisions() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) upload() (galaxy.webapps.tool_shed.controllers.upload.UploadController method) upload_async_create() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) upload_async_message() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) upload_capsule() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) upload_dataset() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) upload_directory() (galaxy.webapps.tool_shed.controllers.upload.UploadController method) upload_library_dataset() (galaxy.webapps.galaxy.controllers.library_common.LibraryCommon method) upload_options (galaxy.model.LibraryDataset attribute) UploadController (class in galaxy.webapps.tool_shed.controllers.upload) UploadDataset (class in galaxy.tools.parameters.grouping)

UploadToolAction (class in galaxy.tools.actions.upload) url (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper attribute) url_for() (galaxy.managers.base.ModelSerializer static method) url_join() (in module tool_shed.util.common_util) url_to_destination() (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.lwr.LwrJobRunner method) url_to_file() (in module galaxy.tools.imp_exp.unpack_tar_gz_archive) urlize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) URLRetriever (class in galaxy.eggs) use_async (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) use_hide_message (galaxy.web.framework.helpers.grids.Grid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) use_paging (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid attribute) (galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.library.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid attribute) (galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid attribute) (galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithNoFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithSkipTestsCheckedGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithTestInstallErrorsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid attribute) (tool_shed.grids.repository_grids.RepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithNoFailingToolTestsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithSkipTestsCheckedGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithTestInstallErrorsGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_grids.ValidRepositoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) use_panels (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (galaxy.webapps.galaxy.controllers.user.UserOpenIDGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) use_pbkdf2 (galaxy.model.User attribute) User (class in galaxy.model) (class in galaxy.webapps.galaxy.controllers.user) (class in galaxy.webapps.tool_shed.model) user (galaxy.jobs.JobWrapper attribute) (galaxy.webapps.tool_shed.model.GalaxySession attribute) (galaxy.webapps.tool_shed.model.PasswordResetToken attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) user_assoc (galaxy.managers.roles.RoleManager attribute) user_can_administer_repository() (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) user_can_browse_component_review() (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) user_can_do_run_as() (galaxy.managers.context.ProvidesUserContext method) user_can_import_repository_archive() (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) user_can_purge (galaxy.model.Dataset attribute) user_can_review_repositories() (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) user_disk_usage() (galaxy.webapps.reports.controllers.users.Users method) user_ftp_dir (galaxy.managers.context.ProvidesUserContext attribute) user_get_default_permissions() (galaxy.security.GalaxyRBACAgent method) user_id (galaxy.webapps.tool_shed.model.APIKeys attribute) (galaxy.webapps.tool_shed.model.GalaxySession attribute) (galaxy.webapps.tool_shed.model.PasswordResetToken attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) user_is_admin() (galaxy.managers.context.ProvidesUserContext method) user_list_grid (galaxy.web.base.controllers.admin.Admin attribute) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (galaxy.webapps.tool_shed.controllers.admin.AdminController attribute) user_openid_grid (galaxy.webapps.galaxy.controllers.user.User attribute) user_per_month() (galaxy.webapps.reports.controllers.jobs.Jobs method) (galaxy.webapps.reports.controllers.sample_tracking.SampleTracking method) (galaxy.webapps.reports.controllers.workflows.Workflows method) user_set_default_permissions() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) user_share_model (galaxy.managers.histories.HistoryManager attribute) user_system_pwent (galaxy.jobs.JobWrapper attribute) user_template_environment() (galaxy.model.User static method) UserAction (class in galaxy.model) UserAddress (class in galaxy.model) UserAPIController (class in galaxy.webapps.galaxy.api.users) UserGrid (class in tool_shed.grids.admin_grids) UserGrid.EmailColumn (class in tool_shed.grids.admin_grids) UserGrid.ExternalColumn (class in tool_shed.grids.admin_grids) UserGrid.GroupsColumn (class in tool_shed.grids.admin_grids) UserGrid.LastLoginColumn (class in tool_shed.grids.admin_grids) UserGrid.RolesColumn (class in tool_shed.grids.admin_grids) UserGrid.StatusColumn (class in tool_shed.grids.admin_grids) UserGrid.UserLoginColumn (class in tool_shed.grids.admin_grids) UserGrid.UserNameColumn (class in tool_shed.grids.admin_grids) UserGroupAssociation (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) userless_histories() (galaxy.webapps.reports.controllers.system.System method) UserListGrid (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.ActivatedColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.EmailColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.ExternalColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.GroupsColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.LastLoginColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.RolesColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.StatusColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.TimeCreatedColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.UserNameColumn (class in galaxy.webapps.galaxy.controllers.admin) username (galaxy.webapps.tool_shed.model.User attribute) UserOpenID (class in galaxy.model) UserOpenIDGrid (class in galaxy.webapps.galaxy.controllers.user) UserPreference (class in galaxy.model) UserQuotaAssociation (class in galaxy.model) UserRequestsGrid (class in galaxy.webapps.galaxy.controllers.requests) UserRoleAssociation (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) Users (class in galaxy.webapps.reports.controllers.users) users (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.Role attribute) users() (galaxy.web.base.controllers.admin.Admin method) uses_tool_shed_dependencies() (galaxy.tools.deps.DependencyManager method) (galaxy.tools.deps.NullDependencyManager method) UsesAnnotations (class in galaxy.model.item_attrs) UsesExtendedMetadataMixin (class in galaxy.web.base.controller) UsesFormDefinitionsMixin (class in galaxy.web.base.controller) UsesItemRatings (class in galaxy.model.item_attrs) UsesLibraryMixin (class in galaxy.web.base.controller) UsesLibraryMixinItems (class in galaxy.web.base.controller) UsesQuotaMixin (class in galaxy.web.base.controller) UsesStoredWorkflowMixin (class in galaxy.web.base.controller) UsesTagsMixin (class in galaxy.web.base.controller) UsesVisualizationMixin (class in galaxy.web.base.controller) UUIDType (class in galaxy.model.custom_types)

V

v (galaxy.webapps.galaxy.api.requests.RequestsAPIController attribute) (galaxy.webapps.galaxy.api.samples.SamplesAPIController attribute) valid_category_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) VALID_FORMATS (galaxy_utils.sequence.fastq.fastqAggregator attribute) valid_gff3_phase (galaxy.datatypes.interval.Gff3 attribute) valid_gff3_strand (galaxy.datatypes.interval.Gff3 attribute) valid_operations (galaxy.model.Quota attribute) VALID_PRESET (galaxy.tools.parameters.sanitize.ToolParameterSanitizer attribute) valid_repository_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) valid_sequence_list (galaxy_utils.sequence.fastq.fastqCSSangerRead attribute) (galaxy_utils.sequence.sequence.SequencingRead attribute) validate() (galaxy.datatypes.data.Data method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.model.DatasetCollection method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.validation.DatasetOkValidator method) (galaxy.tools.parameters.validation.EmptyTextfieldValidator method) (galaxy.tools.parameters.validation.ExpressionValidator method) (galaxy.tools.parameters.validation.InRangeValidator method) (galaxy.tools.parameters.validation.LengthValidator method) (galaxy.tools.parameters.validation.MetadataInDataTableColumnValidator method) (galaxy.tools.parameters.validation.MetadataInFileColumnValidator method) (galaxy.tools.parameters.validation.MetadataValidator method) (galaxy.tools.parameters.validation.NoOptionsValidator method) (galaxy.tools.parameters.validation.RegexValidator method) (galaxy.tools.parameters.validation.UnspecifiedBuildValidator method) (galaxy.tools.parameters.validation.Validator method) validate_email() (in module galaxy.security.validate_user_input) validate_in_users_and_groups() (galaxy.web.base.controller.BaseAPIController method) validate_input_element_identifiers() (in module galaxy.managers.collections_util) validate_jsonrpc_request() (in module galaxy.util.json) validate_jsonrpc_response() (in module galaxy.util.json) validate_password() (in module galaxy.security.validate_user_input) validate_publicname() (in module galaxy.security.validate_user_input) ValidationError (class in galaxy.model) Validator (class in galaxy.tools.parameters.validation) ValidCategoryGrid (class in tool_shed.grids.repository_grids) ValidCategoryGrid.RepositoriesColumn (class in tool_shed.grids.repository_grids) ValidRepositoryGrid (class in tool_shed.grids.repository_grids) ValidRepositoryGrid.CategoryColumn (class in tool_shed.grids.repository_grids) ValidRepositoryGrid.InstallableRevisionColumn (class in tool_shed.grids.repository_grids) ValidRepositoryGrid.RepositoryCategoryColumn (class in tool_shed.grids.repository_grids) value (galaxy_utils.sequence.transform.ColorSpaceConverter attribute) value_from_basic() (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.grouping.Conditional method) (galaxy.tools.parameters.grouping.Group method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.tools.parameters.grouping.UploadDataset method) value_to_basic() (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.grouping.Conditional method) (galaxy.tools.parameters.grouping.Group method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.tools.parameters.grouping.UploadDataset method) value_to_display_text() (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) ValueExternalServiceActionsGroupWhen (class in galaxy.external_services.service) values() (galaxy.util.bunch.Bunch method) (galaxy.util.odict.odict method) ValueToolOutputActionConditionalWhen (class in galaxy.tools.parameters.output) variablize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) VariantCall (class in galaxy_utils.sequence.vcf) VariantCall33 (class in galaxy_utils.sequence.vcf) VariantCall40 (class in galaxy_utils.sequence.vcf) VariantCall41 (class in galaxy_utils.sequence.vcf) Vcf (class in galaxy.datatypes.tabular) Velvet (class in galaxy.datatypes.assembly)

verbose_name (galaxy.jobs.actions.post.ChangeDatatypeAction attribute) (galaxy.jobs.actions.post.ColumnSetAction attribute) (galaxy.jobs.actions.post.DefaultJobAction attribute) (galaxy.jobs.actions.post.DeleteDatasetAction attribute) (galaxy.jobs.actions.post.DeleteIntermediatesAction attribute) (galaxy.jobs.actions.post.EmailAction attribute) (galaxy.jobs.actions.post.HideDatasetAction attribute) (galaxy.jobs.actions.post.RenameDatasetAction attribute) (galaxy.jobs.actions.post.TagDatasetAction attribute) verify_tools() (in module tool_shed.galaxy_install.migrate.check) version (galaxy_utils.sequence.vcf.VariantCall attribute) (galaxy_utils.sequence.vcf.VariantCall33 attribute) (galaxy_utils.sequence.vcf.VariantCall40 attribute) (galaxy_utils.sequence.vcf.VariantCall41 attribute) (pkg_resources.Distribution attribute) version() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method) version_conflict() (galaxy.eggs.Egg method) version_path() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) VersionConflict view() (galaxy.webapps.galaxy.controllers.history.HistoryController method) view_changelog() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) view_changeset() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) view_datatypes_registry() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) view_editable_request_type() (galaxy.webapps.galaxy.controllers.request_type.RequestType method) view_external_service() (galaxy.webapps.galaxy.controllers.external_service.ExternalService method) view_form_definition() (galaxy.webapps.galaxy.controllers.request_type.RequestType method) view_latest_form_definition() (galaxy.webapps.galaxy.controllers.forms.Forms method) view_multiple() (galaxy.webapps.galaxy.controllers.history.HistoryController method) view_or_manage_repository() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) view_repository() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) view_request() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) view_request_history() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) view_request_type() (galaxy.webapps.galaxy.controllers.request_type.RequestType method) view_sample() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) view_sample_datasets() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) view_sample_history() (galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon method) view_tool_data_tables() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) view_tool_metadata() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) view_workflow() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) visible (galaxy.tools.parameters.basic.FTPFileToolParameter attribute) (galaxy.tools.parameters.basic.ToolParameter attribute) (galaxy.tools.parameters.grouping.Group attribute) visit_input_values() (in module galaxy.tools.parameters) visit_inputs() (galaxy.tools.parameters.grouping.Conditional method) (galaxy.tools.Tool method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.tools.parameters.grouping.UploadDataset method) Visualization (class in galaxy.model) VisualizationAnnotationAssociation (class in galaxy.model) VisualizationRatingAssociation (class in galaxy.model) VisualizationRevision (class in galaxy.model) VisualizationsController (class in galaxy.webapps.galaxy.api.visualizations) VisualizationSelectionGrid (class in galaxy.webapps.galaxy.controllers.page) VisualizationTagAssociation (class in galaxy.model) VisualizationUserShareAssociation (class in galaxy.model) viz_types (galaxy.web.base.controller.UsesVisualizationMixin attribute)

W

waiting_for_elements (galaxy.model.DatasetCollection attribute) wake() (galaxy.jobs.deferred.Sleeper method) (galaxy.jobs.transfer_manager.Sleeper method) warn() (in module galaxy.tools.util.galaxyops) WebApplication (class in galaxy.web.framework.base) welcome() (galaxy.webapps.galaxy.controllers.root.RootController method) whoosh_search() (in module galaxy.webapps.galaxy.controllers.library_common) widget_fields_have_contents() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) Wiggle (class in galaxy.datatypes.interval) wiggle_dataprovider() (galaxy.datatypes.interval.Wiggle method) wiggle_dict_dataprovider() (galaxy.datatypes.interval.Wiggle method) Workflow (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) workflow_dict() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) workflow_to_dict() (galaxy.managers.workflows.WorkflowContentsManager method) WorkflowAnnotationsController (class in galaxy.webapps.galaxy.api.annotations) WorkflowContentsManager (class in galaxy.managers.workflows) WorkflowController (class in galaxy.webapps.galaxy.controllers.workflow) WorkflowField (class in galaxy.web.form_builder) WorkflowInvocation (class in galaxy.model) WorkflowInvocationStep (class in galaxy.model) WorkflowMappingField (class in galaxy.web.form_builder) WorkflowModule (class in galaxy.workflow.modules) WorkflowModuleFactory (class in galaxy.workflow.modules) WorkflowModuleInjector (class in galaxy.workflow.modules) WorkflowOutput (class in galaxy.model) WorkflowRequest (class in galaxy.model) WorkflowRequestInputParameter (class in galaxy.model) WorkflowRequestStepState (class in galaxy.model)

WorkflowRequestToInputDatasetAssociation (class in galaxy.model) WorkflowRequestToInputDatasetCollectionAssociation (class in galaxy.model) Workflows (class in galaxy.webapps.reports.controllers.workflows) WorkflowsAPIController (class in galaxy.webapps.galaxy.api.workflows) WorkflowSelectionGrid (class in galaxy.webapps.galaxy.controllers.page) WorkflowsManager (class in galaxy.managers.workflows) WorkflowStep (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) WorkflowStepAnnotationAssociation (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) WorkflowStepConnection (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) WorkflowStepTagAssociation (class in galaxy.model) WorkflowTagsController (class in galaxy.webapps.galaxy.api.item_tags) working_directory() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) WorkingSet (class in pkg_resources) WorkRequestTagAssociation (class in galaxy.model) wrap() (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataElementSpec method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.datatypes.metadata.SelectParameter method) wrap_in_middleware() (in module galaxy.webapps.reports.buildapp) (in module galaxy.webapps.tool_shed.buildapp) wrap_in_static() (in module galaxy.webapps.reports.buildapp) (in module galaxy.webapps.tool_shed.buildapp) writable_files (galaxy.datatypes.data.Data attribute) write() (galaxy.datatypes.converters.interval_to_coverage.CoverageWriter method) (galaxy_utils.sequence.fasta.fastaWriter method) (galaxy_utils.sequence.fastq.fastqWriter method) write_config() (galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager method) write_data_to_file() (galaxy.visualization.data_providers.basic.BaseDataProvider method) write_from_stream() (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Text method) (galaxy.model.DatasetInstance method) write_log() (galaxy.web.framework.middleware.translogger.TransLogger method) write_split_files() (galaxy.datatypes.sequence.Sequence class method) wsgi_headeritems() (galaxy.web.framework.base.Response method) wsgi_status() (galaxy.web.framework.base.Response method) WSGIEnvironmentProperty (class in galaxy.web.framework.base)

X

Xbm (class in galaxy.datatypes.images) XForwardedHostMiddleware (class in galaxy.web.framework.middleware.xforwardedhost) Xlsx (class in galaxy.datatypes.binary) xml_dataprovider() (galaxy.datatypes.xml.GenericXml method) xml_element_compare() (in module galaxy.util) xml_element_list_compare() (in module galaxy.util)

xml_element_to_dict() (in module galaxy.util) xml_string (galaxy.tools.data.TabularToolDataTable attribute) xml_text() (in module galaxy.util) xml_to_string() (in module galaxy.util) Xpm (class in galaxy.datatypes.images)

Y

yield_lines() (in module pkg_resources)

Z

ZipBall (class in galaxy.util.streamball)

ZipProvider (class in pkg_resources)