parameters Package

parameters Package

Classes encapsulating Galaxy tool parameters.

galaxy.tools.parameters.check_param(trans, param, incoming_value, param_values, source='html')

Check the value of a single parameter param. The value in incoming_value is converted from its HTML encoding and validated. The param_values argument contains the processed values of previous parameters (this may actually be an ExpressionContext when dealing with grouping scenarios).

galaxy.tools.parameters.params_from_strings(params, param_values, app, ignore_errors=False)

Convert a dictionary of strings as produced by params_to_strings back into parameter values (decode the json representation and then allow each parameter to convert the basic types into the parameters preferred form).

galaxy.tools.parameters.params_to_incoming(incoming, inputs, input_values, app, name_prefix='', to_html=True)

Given a tool’s parameter definition (inputs) and a specific set of parameter input_values objects, populate incoming with the html values.

Useful for e.g. the rerun function.

galaxy.tools.parameters.params_to_strings(params, param_values, app)

Convert a dictionary of parameter values to a dictionary of strings suitable for persisting. The value_to_basic method of each parameter is called to convert its value to basic types, the result of which is then json encoded (this allowing complex nested parameters and such).

galaxy.tools.parameters.visit_input_values(inputs, input_values, callback, name_prefix='', label_prefix='')

Given a tools parameter definition (inputs) and a specific set of parameter values, call callback for each non-grouping parameter, passing the parameter object, value, a constructed unique name, and a display label.

If the callback returns a value, it will be replace the old value.

FIXME: There is redundancy between this and the visit_inputs methods of

Repeat and Group. This tracks labels and those do not. It would be nice to unify all the places that recursively visit inputs.

basic Module

Basic tool parameters.

class galaxy.tools.parameters.basic.BaseDataToolParameter(tool, input_source, trans)

Bases: galaxy.tools.parameters.basic.ToolParameter

class galaxy.tools.parameters.basic.BaseURLToolParameter(tool, input_source)

Bases: galaxy.tools.parameters.basic.HiddenToolParameter

Returns a parameter that contains its value prepended by the current server base url. Used in all redirects.

from_html(value=None, trans=None, context={})

class galaxy.tools.parameters.basic.BooleanToolParameter(tool, input_source)

Bases: galaxy.tools.parameters.basic.ToolParameter

Parameter that takes one of two values.

>>> p = BooleanToolParameter( None, XML( '<param name="blah" type="boolean" checked="yes" truevalue="bulletproof vests" falsevalue="cellophane chests" />' ) )
>>> print p.name
blah
>>> print p.get_html()
<input type="checkbox" id="blah" name="blah" value="true" checked="checked"><input type="hidden" name="blah" value="true">
>>> print p.from_html( ["true","true"] )
True
>>> print p.to_param_dict_string( True )
bulletproof vests
>>> print p.from_html( ["true"] )
False
>>> print p.to_param_dict_string( False )
cellophane chests

from_html(value, trans=None, other_values={})

from_json(value, trans=None, other_values={})

get_html_field(trans=None, value=None, other_values={})

get_initial_value(trans, context, history=None)

legal_values

to_dict(trans, view='collection', value_mapper=None, other_values={})

to_html_value(value, app)

to_param_dict_string(value, other_values={})

to_python(value, app)

class galaxy.tools.parameters.basic.ColorToolParameter(tool, input_source)

Bases: galaxy.tools.parameters.basic.ToolParameter

Parameter that stores a color.

>>> p = ColorToolParameter( None, XML( '<param name="blah" type="color" value="#ffffff"/>' ) )
>>> print p.name
blah

get_html_field(trans=None, value=None, other_values={})

get_initial_value(trans, context, history=None)

class galaxy.tools.parameters.basic.ColumnListParameter(tool, input_source)

Bases: galaxy.tools.parameters.basic.SelectToolParameter

Select list that consists of either the total number of columns or only those columns that contain numerical values in the associated DataToolParameter.

# TODO: we need better testing here, but not sure how to associate a DatatoolParameter with a ColumnListParameter # from a twill perspective...

>>> # Mock up a history (not connected to database)
>>> from galaxy.model import History, HistoryDatasetAssociation
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.model.mapping import init
>>> sa_session = init( "/tmp", "sqlite:///:memory:", create_tables=True ).session
>>> hist = History()
>>> sa_session.add( hist )
>>> sa_session.flush()
>>> hda = hist.add_dataset( HistoryDatasetAssociation( id=1, extension='interval', create_dataset=True, sa_session=sa_session ) )
>>> dtp =  DataToolParameter( None, XML( '<param name="blah" type="data" format="interval"/>' ) )
>>> print dtp.name
blah
>>> clp = ColumnListParameter ( None, XML( '<param name="numerical_column" type="data_column" data_ref="blah" numerical="true"/>' ) )
>>> print clp.name
numerical_column

from_html(value, trans=None, context={})

Label convention prepends column number with a ‘c’, but tool uses the integer. This removes the ‘c’ when entered into a workflow.

get_column_list(trans, other_values)

Generate a select list containing the columns of the associated dataset (if found).

get_dependencies()

get_initial_value(trans, context, history=None)

get_legal_values(trans, other_values)

get_options(trans, other_values)

show column labels rather than c1..cn if use_header_names=True

to_dict(trans, view='collection', value_mapper=None, other_values={})

galaxy.tools.parameters.basic.DEFAULT_VALUE_MAP(x)

class galaxy.tools.parameters.basic.DataCollectionToolParameter(tool, input_source, trans=None)

Bases: galaxy.tools.parameters.basic.BaseDataToolParameter

collection_type

from_html(value, trans, other_values={})

get_html_field(trans=None, value=None, other_values={})

match_collections(trans, history, dataset_matcher)

match_multirun_collections(trans, history, dataset_matcher)

to_dict(trans, view='collection', value_mapper=None, other_values=None)

to_python(value, app)

to_string(value, app)

validate(value, history=None)

value_to_display_text(value, app)

class galaxy.tools.parameters.basic.DataToolParameter(tool, input_source, trans=None)

Bases: galaxy.tools.parameters.basic.BaseDataToolParameter

Parameter that takes on one (or many) or a specific set of values.

TODO: There should be an alternate display that allows single selects to be

displayed as radio buttons and multiple selects as a set of checkboxes

TODO: The following must be fixed to test correctly for the new security_check tag in the DataToolParameter ( the last test below is broken ) Nate’s next pass at the dataset security stuff will dramatically alter this anyway.

converter_safe(other_values, trans)

from_html(value, trans, other_values={})

get_dependencies()

Get the names of the other params this param depends on.

get_html_field(trans=None, value=None, other_values={})

get_initial_value(trans, context, history=None)

get_initial_value_from_history_prevent_repeats(trans, context, already_used, history=None)

NOTE: This is wasteful since dynamic options and dataset collection

happens twice (here and when generating HTML).

match_collections(history, dataset_matcher, reduction=True)

match_datasets(history, dataset_matcher)

to_dict(trans, view='collection', value_mapper=None, other_values=None)

to_param_dict_string(value, other_values={})

to_python(value, app)

to_string(value, app)

validate(value, history=None)

value_to_display_text(value, app)

class galaxy.tools.parameters.basic.DrillDownSelectToolParameter(tool, input_source, context=None)

Bases: galaxy.tools.parameters.basic.SelectToolParameter

Parameter that takes on one (or many) of a specific set of values. Creating a hierarchical select menu, which allows users to ‘drill down’ a tree-like set of options.

>>> p = DrillDownSelectToolParameter( None, XML(
... '''
... <param name="some_name" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true">
...   <options>
...    <option name="Heading 1" value="heading1">
...        <option name="Option 1" value="option1"/>
...        <option name="Option 2" value="option2"/>
...        <option name="Heading 1" value="heading1">
...          <option name="Option 3" value="option3"/>
...          <option name="Option 4" value="option4"/>
...        </option>
...    </option>
...    <option name="Option 5" value="option5"/>
...   </options>
... </param>
... ''' ) )
>>> print p.get_html()
<div class="form-row drilldown-container" id="drilldown--736f6d655f6e616d65">
<div class="form-row-input">
<div><span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-click"></span>
<input type="checkbox" name="some_name" value="heading1" >Heading 1
</div><div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-container" style="float: left; margin-left: 1em;">
<div class="form-row-input">
<input type="checkbox" name="some_name" value="option1" >Option 1
</div>
<div class="form-row-input">
<input type="checkbox" name="some_name" value="option2" >Option 2
</div>
<div class="form-row-input">
<div><span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-click"></span>
<input type="checkbox" name="some_name" value="heading1" >Heading 1
</div><div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;">
<div class="form-row-input">
<input type="checkbox" name="some_name" value="option3" >Option 3
</div>
<div class="form-row-input">
<input type="checkbox" name="some_name" value="option4" >Option 4
</div>
</div>
</div>
</div>
</div>
<div class="form-row-input">
<input type="checkbox" name="some_name" value="option5" >Option 5
</div>
</div>
>>> p = DrillDownSelectToolParameter( None, XML(
... '''
... <param name="some_name" type="drill_down" display="radio" hierarchy="recurse" multiple="false">
...   <options>
...    <option name="Heading 1" value="heading1">
...        <option name="Option 1" value="option1"/>
...        <option name="Option 2" value="option2"/>
...        <option name="Heading 1" value="heading1">
...          <option name="Option 3" value="option3"/>
...          <option name="Option 4" value="option4"/>
...        </option>
...    </option>
...    <option name="Option 5" value="option5"/>
...   </options>
... </param>
... ''' ) )
>>> print p.get_html()
<div class="form-row drilldown-container" id="drilldown--736f6d655f6e616d65">
<div class="form-row-input">
<div><span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-click"></span>
<input type="radio" name="some_name" value="heading1" >Heading 1
</div><div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-container" style="float: left; margin-left: 1em;">
<div class="form-row-input">
<input type="radio" name="some_name" value="option1" >Option 1
</div>
<div class="form-row-input">
<input type="radio" name="some_name" value="option2" >Option 2
</div>
<div class="form-row-input">
<div><span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-click"></span>
<input type="radio" name="some_name" value="heading1" >Heading 1
</div><div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;">
<div class="form-row-input">
<input type="radio" name="some_name" value="option3" >Option 3
</div>
<div class="form-row-input">
<input type="radio" name="some_name" value="option4" >Option 4
</div>
</div>
</div>
</div>
</div>
<div class="form-row-input">
<input type="radio" name="some_name" value="option5" >Option 5
</div>
</div>
>>> print sorted(p.options[1].items())
[('name', 'Option 5'), ('options', []), ('selected', False), ('value', 'option5')]
>>> p.options[0]["name"]
'Heading 1'
>>> p.options[0]["selected"]
False

from_html(value, trans=None, other_values={})

get_dependencies()

Get the names of the other params this param depends on.

get_html(trans=None, value=None, other_values={})

Returns the html widget corresponding to the paramter. Optionally attempt to retain the current value specific by ‘value’

get_html_field(trans=None, value=None, other_values={})

get_initial_value(trans, context, history=None)

get_legal_values(trans, other_values)

get_options(trans=None, value=None, other_values={})

to_dict(trans, view='collection', value_mapper=None, other_values={})

to_param_dict_string(value, other_values={}, value_map=<function <lambda>>)

value_to_display_text(value, app)

class galaxy.tools.parameters.basic.DummyDataset

Bases: object

class galaxy.tools.parameters.basic.FTPFileToolParameter(tool, input_source)

Bases: galaxy.tools.parameters.basic.ToolParameter

Parameter that takes a file uploaded via FTP as a value.

from_html(value, trans=None, other_values={})

get_html_field(trans=None, value=None, other_values={})

get_initial_value(trans, context, history=None)

to_python(value, app)

to_string(value, app)

visible

class galaxy.tools.parameters.basic.FileToolParameter(tool, input_source)

Bases: galaxy.tools.parameters.basic.ToolParameter

Parameter that takes an uploaded file as a value.

>>> p = FileToolParameter( None, XML( '<param name="blah" type="file"/>' ) )
>>> print p.name
blah
>>> print p.get_html()
<input type="file" name="blah">
>>> p = FileToolParameter( None, XML( '<param name="blah" type="file" ajax-upload="true"/>' ) )
>>> print p.get_html()
<input type="file" name="blah" galaxy-ajax-upload="true">

from_html(value, trans=None, other_values={})

get_html_field(trans=None, value=None, other_values={})

get_initial_value(trans, context, history=None)

get_required_enctype()

File upload elements require the multipart/form-data encoding

to_python(value, app)

to_string(value, app)

class galaxy.tools.parameters.basic.FloatToolParameter(tool, input_source)

Bases: galaxy.tools.parameters.basic.TextToolParameter

Parameter that takes a real number value.

>>> p = FloatToolParameter( None, XML( '<param name="blah" type="float" size="4" value="3.141592" />' ) )
>>> print p.name
blah
>>> print p.get_html()
<input type="text" name="blah" size="4" value="3.141592">
>>> type( p.from_html( "36.1" ) )
<type 'float'>
>>> type( p.from_html( "bleh" ) )
Traceback (most recent call last):
    ...
ValueError: A real number is required

dict_collection_visible_keys = ('name', 'argument', 'type', 'label', 'help', 'min', 'max')

from_html(value, trans=None, other_values={})

get_html_field(trans=None, value=None, other_values={})

get_initial_value(trans, context, history=None)

to_python(value, app)

class galaxy.tools.parameters.basic.GenomeBuildParameter(*args, **kwds)

Bases: galaxy.tools.parameters.basic.SelectToolParameter

Select list that sets the last used genome build for the current history as “selected”.

>>> # Create a mock transaction with 'hg17' as the current build
>>> from galaxy.util.bunch import Bunch
>>> trans = Bunch( history=Bunch( genome_build='hg17' ), db_builds=util.read_dbnames( None ) )

>>> p = GenomeBuildParameter( None, XML(
... '''
... <param name="blah" type="genomebuild" />
... ''' ) )
>>> print p.name
blah

>>> # hg17 should be selected by default
>>> print p.get_html( trans ) 
<select name="blah" last_selected_value="hg17">
<option value="?">unspecified (?)</option>
...
<option value="hg18">Human Mar. 2006 (NCBI36/hg18) (hg18)</option>
<option value="hg17" selected>Human May 2004 (NCBI35/hg17) (hg17)</option>
...
</select>

>>> # If the user selected something else already, that should be used
>>> # instead
>>> print p.get_html( trans, value='hg18' ) 
<select name="blah" last_selected_value="hg18">
<option value="?">unspecified (?)</option>
...
<option value="hg18" selected>Human Mar. 2006 (NCBI36/hg18) (hg18)</option>
<option value="hg17">Human May 2004 (NCBI35/hg17) (hg17)</option>
...
</select>

>>> print p.filter_value( "hg17" )
hg17

get_legal_values(trans, other_values)

get_options(trans, other_values)

to_dict(trans, view='collection', value_mapper=None, other_values={})

class galaxy.tools.parameters.basic.HiddenDataToolParameter(tool, elem)

Bases: galaxy.tools.parameters.basic.HiddenToolParameter, galaxy.tools.parameters.basic.DataToolParameter

Hidden parameter that behaves as a DataToolParameter. As with all hidden parameters, this is a HACK.

get_html_field(trans=None, value=None, other_values={})

get_initial_value(trans, context, history=None)

class galaxy.tools.parameters.basic.HiddenToolParameter(tool, input_source)

Bases: galaxy.tools.parameters.basic.ToolParameter

Parameter that takes one of two values.

FIXME: This seems hacky, parameters should only describe things the user

might change. It is used for ‘initializing’ the UCSC proxy tool

>>> p = HiddenToolParameter( None, XML( '<param name="blah" type="hidden" value="wax so rockin"/>' ) )
>>> print p.name
blah
>>> print p.get_html()
<input type="hidden" name="blah" value="wax so rockin">

get_html_field(trans=None, value=None, other_values={})

get_initial_value(trans, context, history=None)

get_label()

class galaxy.tools.parameters.basic.IntegerToolParameter(tool, input_source)

Bases: galaxy.tools.parameters.basic.TextToolParameter

Parameter that takes an integer value.

>>> p = IntegerToolParameter( None, XML( '<param name="blah" type="integer" size="4" value="10" />' ) )
>>> print p.name
blah
>>> print p.get_html()
<input type="text" name="blah" size="4" value="10">
>>> type( p.from_html( "10" ) )
<type 'int'>
>>> type( p.from_html( "bleh" ) )
Traceback (most recent call last):
    ...
ValueError: An integer is required

dict_collection_visible_keys = ('name', 'argument', 'type', 'label', 'help', 'min', 'max')

from_html(value, trans=None, other_values={})

get_html_field(trans=None, value=None, other_values={})

get_initial_value(trans, context, history=None)

to_python(value, app)

class galaxy.tools.parameters.basic.LibraryDatasetToolParameter(tool, elem)

Bases: galaxy.tools.parameters.basic.ToolParameter

Parameter that lets users select a LDDA from a modal window, then use it within the wrapper.

from_html(value, trans, other_values={})

get_html_field(trans=None, value=None, other_values={})

get_initial_value(trans, context, history=None)

to_python(value, app)

to_string(value, app)

class galaxy.tools.parameters.basic.RuntimeValue

Bases: object

Wrapper to note a value that is not yet set, but will be required at runtime.

class galaxy.tools.parameters.basic.SelectToolParameter(tool, input_source, context=None)

Bases: galaxy.tools.parameters.basic.ToolParameter

Parameter that takes on one (or many) or a specific set of values.

>>> p = SelectToolParameter( None, XML(
... '''
... <param name="blah" type="select">
...     <option value="x">I am X</option>
...     <option value="y" selected="true">I am Y</option>
...     <option value="z">I am Z</option>
... </param>
... ''' ) )
>>> print p.name
blah
>>> print p.get_html()
<select name="blah" last_selected_value="y">
<option value="x">I am X</option>
<option value="y" selected>I am Y</option>
<option value="z">I am Z</option>
</select>
>>> print p.get_html( value="z" )
<select name="blah" last_selected_value="z">
<option value="x">I am X</option>
<option value="y">I am Y</option>
<option value="z" selected>I am Z</option>
</select>
>>> print p.filter_value( "y" )
y

>>> p = SelectToolParameter( None, XML(
... '''
... <param name="blah" type="select" multiple="true">
...     <option value="x">I am X</option>
...     <option value="y" selected="true">I am Y</option>
...     <option value="z" selected="true">I am Z</option>
... </param>
... ''' ) )
>>> print p.name
blah
>>> print p.get_html()
<select name="blah" multiple last_selected_value="z">
<option value="x">I am X</option>
<option value="y" selected>I am Y</option>
<option value="z" selected>I am Z</option>
</select>
>>> print p.get_html( value=["x","y"])
<select name="blah" multiple last_selected_value="y">
<option value="x" selected>I am X</option>
<option value="y" selected>I am Y</option>
<option value="z">I am Z</option>
</select>
>>> print p.to_param_dict_string( ["y", "z"] )
y,z

>>> p = SelectToolParameter( None, XML(
... '''
... <param name="blah" type="select" multiple="true" display="checkboxes">
...     <option value="x">I am X</option>
...     <option value="y" selected="true">I am Y</option>
...     <option value="z" selected="true">I am Z</option>
... </param>
... ''' ) )
>>> print p.name
blah
>>> print p.get_html()
<div class="checkUncheckAllPlaceholder" checkbox_name="blah"></div>
<div><input type="checkbox" name="blah" value="x" id="blah|x"><label class="inline" for="blah|x">I am X</label></div>
<div class="odd_row"><input type="checkbox" name="blah" value="y" id="blah|y" checked='checked'><label class="inline" for="blah|y">I am Y</label></div>
<div><input type="checkbox" name="blah" value="z" id="blah|z" checked='checked'><label class="inline" for="blah|z">I am Z</label></div>
>>> print p.get_html( value=["x","y"])
<div class="checkUncheckAllPlaceholder" checkbox_name="blah"></div>
<div><input type="checkbox" name="blah" value="x" id="blah|x" checked='checked'><label class="inline" for="blah|x">I am X</label></div>
<div class="odd_row"><input type="checkbox" name="blah" value="y" id="blah|y" checked='checked'><label class="inline" for="blah|y">I am Y</label></div>
<div><input type="checkbox" name="blah" value="z" id="blah|z"><label class="inline" for="blah|z">I am Z</label></div>
>>> print p.to_param_dict_string( ["y", "z"] )
y,z

from_html(value, trans=None, context={})

get_dependencies()

Get the names of the other params this param depends on.

get_html_field(trans=None, value=None, context={})

get_initial_value(trans, context, history=None)

get_legal_values(trans, other_values)

get_options(trans, other_values)

to_dict(trans, view='collection', value_mapper=None, other_values={})

to_html_value(value, app)

to_param_dict_string(value, other_values={}, value_map=<function <lambda>>)

value_from_basic(value, app, ignore_errors=False)

value_to_basic(value, app)

value_to_display_text(value, app)

class galaxy.tools.parameters.basic.TextToolParameter(tool, input_source)

Bases: galaxy.tools.parameters.basic.ToolParameter

Parameter that can take on any text value.

>>> p = TextToolParameter( None, XML( '<param name="blah" type="text" size="4" value="default" />' ) )
>>> print p.name
blah
>>> print p.get_html()
<input type="text" name="blah" size="4" value="default">
>>> print p.get_html( value="meh" )
<input type="text" name="blah" size="4" value="meh">

get_html_field(trans=None, value=None, other_values={})

get_initial_value(trans, context, history=None)

to_dict(trans, view='collection', value_mapper=None, other_values={})

to_html_value(value, app)

to_string(value, app)

Convert a value to a string representation suitable for persisting

class galaxy.tools.parameters.basic.ToolParameter(tool, input_source, context=None)

Bases: object, galaxy.model.item_attrs.Dictifiable

Describes a parameter accepted by a tool. This is just a simple stub at the moment but in the future should encapsulate more complex parameters (lists of valid choices, validation logic, ...)

classmethod build(tool, param)

Factory method to create parameter of correct type

dict_collection_visible_keys = ('name', 'argument', 'type', 'label', 'help')

filter_value(value, trans=None, other_values={})

Parse the value returned by the view into a form usable by the tool OR raise a ValueError.

from_html(value, trans=None, other_values={})

Convert a value from an HTML POST into the parameters preferred value format.

from_json(value, trans=None, other_values={})

get_dependencies()

Return the names of any other parameters this parameter depends on

get_html(trans=None, value=None, other_values={})

Returns the html widget corresponding to the parameter. Optionally attempt to retain the current value specific by ‘value’

get_html_field(trans=None, value=None, other_values={})

get_initial_value(trans, context, history=None)

Return the starting value of the parameter

get_initial_value_from_history_prevent_repeats(trans, context, already_used, history=None)

Get the starting value for the parameter, but if fetching from the history, try to find a value that has not yet been used. already_used is a list of objects that tools must manipulate (by adding to it) to store a memento that they can use to detect if a value has already been chosen from the history. This is to support the capability to choose each dataset once

get_label()

Return user friendly name for the parameter

get_required_enctype()

If this parameter needs the form to have a specific encoding return it, otherwise return None (indicating compatibility with any encoding)

classmethod parse_name(input_source)

to_dict(trans, view='collection', value_mapper=None, other_values={})

to_dict tool parameter. This can be overridden by subclasses.

to_html_value(value, app)

Convert an object value to the value expected from an html post

to_param_dict_string(value, other_values={})

Called via __str__ when used in the Cheetah template

to_python(value, app)

Convert a value created with to_string back to an object representation

to_string(value, app)

Convert a value to a string representation suitable for persisting

validate(value, history=None)

value_from_basic(value, app, ignore_errors=False)

value_to_basic(value, app)

value_to_display_text(value, app)

Convert a value to a text representation suitable for displaying to the user

visible

Return true if the parameter should be rendered on the form

class galaxy.tools.parameters.basic.UnvalidatedValue(value)

Bases: object

Wrapper to mark a value that has not been validated

dynamic_options Module

Support for generating the options for a SelectToolParameter dynamically (based on the values of other parameters or other aspects of the current state)

class galaxy.tools.parameters.dynamic_options.AdditionalValueFilter(d_option, elem)

Bases: galaxy.tools.parameters.dynamic_options.Filter

Adds a single static value to an options list.

Type: add_value

Required Attributes:

value: value to appear in select list

Optional Attributes:

name: Display name to appear in select list (value) index: Index of option list to add value (APPEND)

filter_options(options, trans, other_values)

class galaxy.tools.parameters.dynamic_options.AttributeValueSplitterFilter(d_option, elem)

Bases: galaxy.tools.parameters.dynamic_options.Filter

Filters a list of attribute-value pairs to be unique attribute names.

Type: attribute_value_splitter

Required Attributes:

column: column in options to compare with

Optional Attributes:

pair_separator: Split column by this (,) name_val_separator: Split name-value pair by this ( whitespace )

filter_options(options, trans, other_values)

class galaxy.tools.parameters.dynamic_options.DataMetaFilter(d_option, elem)

Bases: galaxy.tools.parameters.dynamic_options.Filter

Filters a list of options on a column by a dataset metadata value.

Type: data_meta

When no ‘from’ source has been specified in the <options> tag, this will populate the options list with (meta_value, meta_value, False). Otherwise, options which do not match the metadata value in the column are discarded.

Required Attributes:

• ref: Name of input dataset
• key: Metadata key to use for comparison
• column: column in options to compare with (not required when not associated with input options)

Optional Attributes:

• multiple: Option values are multiple, split column by separator (True)
• separator: When multiple split by this (,)

filter_options(options, trans, other_values)

get_dependency_name()

class galaxy.tools.parameters.dynamic_options.DynamicOptions(elem, tool_param)

Bases: object

Handles dynamically generated SelectToolParameter options

column_spec_to_index(column_spec)

Convert a column specification (as read from the config file), to an index. A column specification can just be a number, a column name, or a column alias.

get_dependency_names()

Return the names of parameters these options depend on – both data and other param types.

get_field_by_name_for_value(field_name, value, trans, other_values)

Get contents of field by name for specified value.

get_fields(trans, other_values)

get_fields_by_value(value, trans, other_values)

Return a list of fields with column ‘value’ matching provided value.

get_options(trans, other_values)

parse_column_definitions(elem)

parse_file_fields(reader)

class galaxy.tools.parameters.dynamic_options.Filter(d_option, elem)

Bases: object

A filter takes the current options list and modifies it.

filter_options(options, trans, other_values)

Returns a list of options after the filter is applied

classmethod from_element(d_option, elem)

Loads the proper filter by the type attribute of elem

get_dependency_name()

Returns the name of any depedencies, otherwise None

class galaxy.tools.parameters.dynamic_options.MultipleSplitterFilter(d_option, elem)

Bases: galaxy.tools.parameters.dynamic_options.Filter

Turns a single line of options into multiple lines, by splitting a column and creating a line for each item.

Type: multiple_splitter

Required Attributes:

column: column in options to compare with

Optional Attributes:

separator: Split column by this (,)

filter_options(options, trans, other_values)

class galaxy.tools.parameters.dynamic_options.ParamValueFilter(d_option, elem)

Bases: galaxy.tools.parameters.dynamic_options.Filter

Filters a list of options on a column by the value of another input.

Type: param_value

Required Attributes:

• ref: Name of input value
• column: column in options to compare with

Optional Attributes:

• keep: Keep columns matching value (True)

  Discard columns matching value (False)

• ref_attribute: Period (.) separated attribute chain of input (ref) to use as value for filter

filter_options(options, trans, other_values)

get_dependency_name()

class galaxy.tools.parameters.dynamic_options.RemoveValueFilter(d_option, elem)

Bases: galaxy.tools.parameters.dynamic_options.Filter

Removes a value from an options list.

Type: remove_value

Required Attributes:

value: value to remove from select list
    or
ref: param to refer to
    or
meta_ref: dataset to refer to
key: metadata key to compare to

filter_options(options, trans, other_values)

class galaxy.tools.parameters.dynamic_options.SortByColumnFilter(d_option, elem)

Bases: galaxy.tools.parameters.dynamic_options.Filter

Sorts an options list by a column

Type: sort_by

Required Attributes:

column: column to sort by

filter_options(options, trans, other_values)

class galaxy.tools.parameters.dynamic_options.StaticValueFilter(d_option, elem)

Bases: galaxy.tools.parameters.dynamic_options.Filter

Filters a list of options on a column by a static value.

Type: static_value

Required Attributes:

value: static value to compare to column: column in options to compare with

Optional Attributes:

keep: Keep columns matching value (True)

Discard columns matching value (False)

filter_options(options, trans, other_values)

class galaxy.tools.parameters.dynamic_options.UniqueValueFilter(d_option, elem)

Bases: galaxy.tools.parameters.dynamic_options.Filter

Filters a list of options to be unique by a column value.

Type: unique_value

Required Attributes:

column: column in options to compare with

filter_options(options, trans, other_values)

get_dependency_name()

grouping Module

Constructs for grouping tool parameters

class galaxy.tools.parameters.grouping.Conditional

Bases: galaxy.tools.parameters.grouping.Group

get_current_case(value, trans)

get_initial_value(trans, context, history=None)

is_job_resource_conditional

label

to_dict(trans, view='collection', value_mapper=None)

type = 'conditional'

value_from_basic(value, app, ignore_errors=False)

value_to_basic(value, app)

visit_inputs(prefix, value, callback)

class galaxy.tools.parameters.grouping.ConditionalWhen

Bases: object, galaxy.model.item_attrs.Dictifiable

dict_collection_visible_keys = ('value',)

to_dict(trans, view='collection', value_mapper=None)

class galaxy.tools.parameters.grouping.Group

Bases: object, galaxy.model.item_attrs.Dictifiable

dict_collection_visible_keys = ('name', 'type')

get_initial_value(trans, context, history=None)

Return the initial state/value for this group

to_dict(trans, view='collection', value_mapper=None)

value_from_basic(value, app, ignore_errors=False)

Convert a basic representation as produced by value_to_basic back into the preferred value form.

value_to_basic(value, app)

Convert value to a (possibly nested) representation using only basic types (dict, list, tuple, str, unicode, int, long, float, bool, None)

visible

class galaxy.tools.parameters.grouping.Repeat

Bases: galaxy.tools.parameters.grouping.Group

dict_collection_visible_keys = ('name', 'type', 'title', 'help', 'default', 'min', 'max')

get_initial_value(trans, context, history=None)

label()

title_plural

to_dict(trans, view='collection', value_mapper=None)

type = 'repeat'

value_from_basic(value, app, ignore_errors=False)

value_to_basic(value, app)

visit_inputs(prefix, value, callback)

class galaxy.tools.parameters.grouping.Section

Bases: galaxy.tools.parameters.grouping.Group

dict_collection_visible_keys = ('name', 'type', 'title', 'help', 'expanded')

get_initial_value(trans, context, history=None)

label()

title_plural

to_dict(trans, view='collection', value_mapper=None)

type = 'section'

value_from_basic(value, app, ignore_errors=False)

value_to_basic(value, app)

visit_inputs(prefix, value, callback)

class galaxy.tools.parameters.grouping.UploadDataset

Bases: galaxy.tools.parameters.grouping.Group

get_composite_dataset_name(context)

get_datatype(trans, context)

get_datatype_ext(trans, context)

get_file_base_name(context)

get_file_type(context)

get_initial_value(trans, context, history=None)

get_uploaded_datasets(trans, context, override_name=None, override_info=None)

group_title(context)

title_by_index(trans, index, context)

title_plural

type = 'upload_dataset'

value_from_basic(value, app, ignore_errors=False)

value_to_basic(value, app)

visit_inputs(prefix, value, callback)

input_translation Module

Tool Input Translation.

class galaxy.tools.parameters.input_translation.ToolInputTranslator

Bases: object

Handles Tool input translation. This is used for data source tools

>>> from galaxy.util import Params
>>> from xml.etree.ElementTree import XML
>>> translator = ToolInputTranslator.from_element( XML(
... '''
... <request_param_translation>
...  <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
...  <request_param galaxy_name="URL" remote_name="URL" missing="" >
...     <append_param separator="&amp;" first_separator="?" join="=">
...         <value name="_export" missing="1" />
...         <value name="GALAXY_URL" missing="0" />
...     </append_param>
...  </request_param>
...  <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
...  <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
...  <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
...  <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
...  <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" >
...   <value_translation>
...    <value galaxy_value="tabular" remote_value="primaryTable" />
...    <value galaxy_value="tabular" remote_value="selectedFields" />
...    <value galaxy_value="wig" remote_value="wigData" />
...    <value galaxy_value="interval" remote_value="tab" />
...    <value galaxy_value="html" remote_value="hyperlinks" />
...    <value galaxy_value="fasta" remote_value="sequence" />
...   </value_translation>
...  </request_param>
... </request_param_translation>
... ''' ) )
>>> params = Params( { 'db':'hg17', 'URL':'URL_value', 'org':'Human', 'hgta_outputType':'primaryTable'  } )
>>> translator.translate( params )
>>> print sorted(list(params.__dict__.keys()))
['URL', 'URL_method', 'data_type', 'db', 'dbkey', 'description', 'hgta_outputType', 'org', 'organism', 'table']
>>> params.get('URL', None) in ['URL_value?GALAXY_URL=0&_export=1', 'URL_value?_export=1&GALAXY_URL=0']
True

classmethod from_element(elem)

Loads the proper filter by the type attribute of elem

translate(params)

update params in-place

output Module

Support for dynamically modifying output attributes.

class galaxy.tools.parameters.output.BooleanFilter(parent, elem)

Bases: galaxy.tools.parameters.output.ToolOutputActionOptionFilter

filter_options(options, other_values)

tag = 'boolean'

class galaxy.tools.parameters.output.ColumnReplaceFilter(parent, elem)

Bases: galaxy.tools.parameters.output.ToolOutputActionOptionFilter

filter_options(options, other_values)

tag = 'column_replace'

class galaxy.tools.parameters.output.ColumnStripFilter(parent, elem)

Bases: galaxy.tools.parameters.output.ToolOutputActionOptionFilter

filter_options(options, other_values)

tag = 'column_strip'

class galaxy.tools.parameters.output.DatatypeIsInstanceToolOutputActionConditionalWhen(parent, config_elem, value)

Bases: galaxy.tools.parameters.output.ToolOutputActionConditionalWhen

is_case(output_dataset, other_values)

tag = 'when datatype_isinstance'

class galaxy.tools.parameters.output.FormatToolOutputAction(parent, elem)

Bases: galaxy.tools.parameters.output.ToolOutputAction

apply_action(output_dataset, other_values)

tag = 'format'

class galaxy.tools.parameters.output.FromDataTableOutputActionOption(parent, elem)

Bases: galaxy.tools.parameters.output.ToolOutputActionOption

get_value(other_values)

tag = 'from_data_table'

class galaxy.tools.parameters.output.FromFileToolOutputActionOption(parent, elem)

Bases: galaxy.tools.parameters.output.ToolOutputActionOption

get_value(other_values)

tag = 'from_file'

class galaxy.tools.parameters.output.FromParamToolOutputActionOption(parent, elem)

Bases: galaxy.tools.parameters.output.ToolOutputActionOption

get_value(other_values)

tag = 'from_param'

class galaxy.tools.parameters.output.InsertColumnToolOutputActionOptionFilter(parent, elem)

Bases: galaxy.tools.parameters.output.ToolOutputActionOptionFilter

filter_options(options, other_values)

tag = 'insert_column'

class galaxy.tools.parameters.output.MetadataToolOutputAction(parent, elem)

Bases: galaxy.tools.parameters.output.ToolOutputAction

apply_action(output_dataset, other_values)

tag = 'metadata'

class galaxy.tools.parameters.output.MetadataValueFilter(parent, elem)

Bases: galaxy.tools.parameters.output.ToolOutputActionOptionFilter

filter_options(options, other_values)

tag = 'metadata_value'

class galaxy.tools.parameters.output.MultipleSplitterFilter(parent, elem)

Bases: galaxy.tools.parameters.output.ToolOutputActionOptionFilter

filter_options(options, other_values)

tag = 'multiple_splitter'

class galaxy.tools.parameters.output.NullToolOutputActionOption(parent, elem)

Bases: galaxy.tools.parameters.output.ToolOutputActionOption

get_value(other_values)

tag = 'null_option'

class galaxy.tools.parameters.output.ParamValueToolOutputActionOptionFilter(parent, elem)

Bases: galaxy.tools.parameters.output.ToolOutputActionOptionFilter

filter_options(options, other_values)

tag = 'param_value'

class galaxy.tools.parameters.output.StringFunctionFilter(parent, elem)

Bases: galaxy.tools.parameters.output.ToolOutputActionOptionFilter

filter_options(options, other_values)

tag = 'string_function'

class galaxy.tools.parameters.output.ToolOutputAction(parent, elem)

Bases: object

apply_action(output_dataset, other_values)

classmethod from_elem(parent, elem)

Loads the proper action by the type attribute of elem

tag = 'action'

tool

class galaxy.tools.parameters.output.ToolOutputActionConditional(parent, config_elem)

Bases: object

apply_action(output_dataset, other_values)

tag = 'conditional'

tool

class galaxy.tools.parameters.output.ToolOutputActionConditionalWhen(parent, config_elem, value)

Bases: galaxy.tools.parameters.output.ToolOutputActionGroup

apply_action(output_dataset, other_values)

classmethod from_elem(parent, when_elem)

Loads the proper when by attributes of elem

get_ref(output_dataset, other_values)

is_case(output_dataset, other_values)

tag = 'when'

class galaxy.tools.parameters.output.ToolOutputActionGroup(parent, config_elem)

Bases: object

Manages a set of tool output dataset actions directives

apply_action(output_dataset, other_values)

tag = 'group'

tool

class galaxy.tools.parameters.output.ToolOutputActionOption(parent, elem)

Bases: object

classmethod from_elem(parent, elem)

Loads the proper action by the type attribute of elem

get_value(other_values)

tag = 'object'

tool

class galaxy.tools.parameters.output.ToolOutputActionOptionFilter(parent, elem)

Bases: object

filter_options(options, other_values)

classmethod from_elem(parent, elem)

Loads the proper action by the type attribute of elem

tag = 'filter'

tool

class galaxy.tools.parameters.output.ValueToolOutputActionConditionalWhen(parent, config_elem, value)

Bases: galaxy.tools.parameters.output.ToolOutputActionConditionalWhen

is_case(output_dataset, other_values)

tag = 'when value'

galaxy.tools.parameters.output.action_type

alias of FormatToolOutputAction

galaxy.tools.parameters.output.compare_endswith(value1, value2)

galaxy.tools.parameters.output.compare_eq(value1, value2)

galaxy.tools.parameters.output.compare_gt(value1, value2)

galaxy.tools.parameters.output.compare_gte(value1, value2)

galaxy.tools.parameters.output.compare_in(value1, value2)

galaxy.tools.parameters.output.compare_lt(value1, value2)

galaxy.tools.parameters.output.compare_lte(value1, value2)

galaxy.tools.parameters.output.compare_neq(value1, value2)

galaxy.tools.parameters.output.compare_re_search(value1, value2)

galaxy.tools.parameters.output.compare_startswith(value1, value2)

galaxy.tools.parameters.output.filter_type

alias of ColumnReplaceFilter

galaxy.tools.parameters.output.option_type

alias of FromDataTableOutputActionOption

galaxy.tools.parameters.output.parse_cast_attribute(cast)

galaxy.tools.parameters.output.parse_compare_type(compare)

sanitize Module

Tool Parameter specific sanitizing.

class galaxy.tools.parameters.sanitize.ToolParameterSanitizer

Bases: object

Handles tool parameter specific sanitizing.

>>> from xml.etree.ElementTree import XML
>>> sanitizer = ToolParameterSanitizer.from_element( XML(
... '''
... <sanitizer invalid_char="">
...   <valid initial="string.letters"/>
... </sanitizer>
... ''' ) )
>>> sanitizer.sanitize_param( ''.join( sorted( [ c for c in string.printable ] ) ) ) == ''.join( sorted( [ c for c in string.letters ] ) )
True
>>> slash = chr( 92 )
>>> sanitizer = ToolParameterSanitizer.from_element( XML(
... '''
... <sanitizer>
...   <valid initial="none">
...    <add preset="string.printable"/>
...    <remove value="&quot;"/>
...    <remove value="%s"/>
...   </valid>
...   <mapping initial="none">
...     <add source="&quot;" target="%s&quot;"/>
...     <add source="%s" target="%s%s"/>
...   </mapping>
... </sanitizer>
... ''' % ( slash, slash, slash, slash, slash ) ) )
>>> text = '%s"$rm&#!' % slash
>>> [ c for c in sanitizer.sanitize_param( text ) ] == [ slash, slash, slash, '"', '$', 'r', 'm', '&', '#', '!' ]
True

DEFAULT_INVALID_CHAR = 'X'

MAPPING_PRESET = {'default': {'@': '__at__', '\t': '__tc__', '\n': '__cn__', '\r': '__cr__', '[': '__ob__', ']': '__cb__', '#': '__pd__', '"': '__dq__', "'": '__sq__', '{': '__oc__', '}': '__cc__', '<': '__lt__', '>': '__gt__'}, 'none': {}}

VALID_PRESET = {'default': 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789 -=_.()/+*^,:?!', 'none': ''}

classmethod from_element(elem)

Loads the proper filter by the type attribute of elem

classmethod get_mapping_by_name(name)

classmethod get_valid_by_name(name)

restore_param(value)

restore_text(text)

Restores sanitized text

sanitize_param(value)

Clean incoming parameters (strings or lists)

sanitize_text(text)

Restricts the characters that are allowed in a text

validation Module

Classes related to parameter validation.

class galaxy.tools.parameters.validation.DatasetOkValidator(message=None)

Bases: galaxy.tools.parameters.validation.Validator

Validator that checks if a dataset is in an ‘ok’ state

classmethod from_element(param, elem)

validate(value, history=None)

class galaxy.tools.parameters.validation.EmptyTextfieldValidator(message=None)

Bases: galaxy.tools.parameters.validation.Validator

Validator that checks for empty text field

classmethod from_element(param, elem)

validate(value, history=None)

class galaxy.tools.parameters.validation.ExpressionValidator(message, expression, substitute_value_in_message)

Bases: galaxy.tools.parameters.validation.Validator

Validator that evaluates a python expression using the value

>>> from galaxy.tools.parameters import ToolParameter
>>> p = ToolParameter.build( None, XML( '''
... <param name="blah" type="text" size="10" value="10">
...     <validator type="expression" message="Not gonna happen">value.lower() == "foo"</validator>
... </param>
... ''' ) )
>>> t = p.validate( "Foo" )
>>> t = p.validate( "foo" )
>>> t = p.validate( "Fop" )
Traceback (most recent call last):
    ...
ValueError: Not gonna happen

classmethod from_element(param, elem)

validate(value, history=None)

class galaxy.tools.parameters.validation.InRangeValidator(message, range_min, range_max)

Bases: galaxy.tools.parameters.validation.Validator

Validator that ensures a number is in a specific range

>>> from galaxy.tools.parameters import ToolParameter
>>> p = ToolParameter.build( None, XML( '''
... <param name="blah" type="integer" size="10" value="10">
...     <validator type="in_range" message="Not gonna happen" min="10" max="20"/>
... </param>
... ''' ) )
>>> t = p.validate( 10 )
>>> t = p.validate( 15 )
>>> t = p.validate( 20 )
>>> t = p.validate( 21 )
Traceback (most recent call last):
    ...
ValueError: Not gonna happen

classmethod from_element(param, elem)

validate(value, history=None)

exception galaxy.tools.parameters.validation.LateValidationError(message)

Bases: exceptions.Exception

class galaxy.tools.parameters.validation.LengthValidator(message, length_min, length_max)

Bases: galaxy.tools.parameters.validation.Validator

Validator that ensures the length of the provided string (value) is in a specific range

>>> from galaxy.tools.parameters import ToolParameter
>>> p = ToolParameter.build( None, XML( '''
... <param name="blah" type="text" size="10" value="foobar">
...     <validator type="length" min="2" max="8"/>
... </param>
... ''' ) )
>>> t = p.validate( "foo" )
>>> t = p.validate( "bar" )
>>> t = p.validate( "f" )
Traceback (most recent call last):
    ...
ValueError: Must have length of at least 2
>>> t = p.validate( "foobarbaz" )
Traceback (most recent call last):
    ...
ValueError: Must have length no more than 8

classmethod from_element(param, elem)

validate(value, history=None)

class galaxy.tools.parameters.validation.MetadataInDataTableColumnValidator(tool_data_table, metadata_name, metadata_column, message='Value for metadata not found.', line_startswith=None)

Bases: galaxy.tools.parameters.validation.Validator

Validator that checks if the value for a dataset’s metadata item exists in a file.

classmethod from_element(param, elem)

validate(value, history=None)

class galaxy.tools.parameters.validation.MetadataInFileColumnValidator(filename, metadata_name, metadata_column, message='Value for metadata not found.', line_startswith=None)

Bases: galaxy.tools.parameters.validation.Validator

Validator that checks if the value for a dataset’s metadata item exists in a file.

classmethod from_element(param, elem)

validate(value, history=None)

class galaxy.tools.parameters.validation.MetadataValidator(message=None, check='', skip='')

Bases: galaxy.tools.parameters.validation.Validator

Validator that checks for missing metadata

classmethod from_element(param, elem)

validate(value, history=None)

class galaxy.tools.parameters.validation.NoOptionsValidator(message=None)

Bases: galaxy.tools.parameters.validation.Validator

Validator that checks for empty select list

classmethod from_element(param, elem)

validate(value, history=None)

class galaxy.tools.parameters.validation.RegexValidator(message, expression)

Bases: galaxy.tools.parameters.validation.Validator

Validator that evaluates a regular expression

>>> from galaxy.tools.parameters import ToolParameter
>>> p = ToolParameter.build( None, XML( '''
... <param name="blah" type="text" size="10" value="10">
...     <validator type="regex" message="Not gonna happen">[Ff]oo</validator>
... </param>
... ''' ) )
>>> t = p.validate( "Foo" )
>>> t = p.validate( "foo" )
>>> t = p.validate( "Fop" )
Traceback (most recent call last):
    ...
ValueError: Not gonna happen

classmethod from_element(param, elem)

validate(value, history=None)

class galaxy.tools.parameters.validation.UnspecifiedBuildValidator(message=None)

Bases: galaxy.tools.parameters.validation.Validator

Validator that checks for dbkey not equal to ‘?’

classmethod from_element(param, elem)

validate(value, history=None)

class galaxy.tools.parameters.validation.Validator

Bases: object

A validator checks that a value meets some conditions OR raises ValueError

classmethod from_element(param, elem)

validate(value, history=None)

galaxy.tools.parameters.validation.get_suite()

Get unittest suite for this module