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galaxy.tools.parameters package

Classes encapsulating Galaxy tool parameters.

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

Bases: galaxy.tools.parameters.basic.BaseDataToolParameter

__init__(tool, input_source, trans=None)

collection_types

match_collections(trans, history, dataset_collection_matcher)

match_multirun_collections(trans, history, dataset_collection_matcher)

from_json(value, trans, other_values={})

to_text(value)

validate(value, trans=None)

to_dict(trans, other_values=None)

class galaxy.tools.parameters.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.

__init__(tool, input_source, trans=None)

from_json(value, trans, other_values={})

to_param_dict_string(value, other_values={})

to_text(value)

validate(value, trans=None)

get_dependencies()

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

converter_safe(other_values, trans)

get_options_filter_attribute(value)

to_dict(trans, other_values={})

class galaxy.tools.parameters.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.

>>> from galaxy.util.bunch import Bunch
>>> trans = Bunch(app=None, history=Bunch(), workflow_building_mode=False)
>>> p = SelectToolParameter(None, XML(
... '''
... <param name="_name" type="select">
...     <option value="x">x_label</option>
...     <option value="y" selected="true">y_label</option>
...     <option value="z">z_label</option>
... </param>
... '''))
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('argument', None), ('display', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', False), ('name', '_name'), ('optional', False), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', False)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', 'y')]
>>> p = SelectToolParameter(None, XML(
... '''
... <param name="_name" type="select" multiple="true">
...     <option value="x">x_label</option>
...     <option value="y" selected="true">y_label</option>
...     <option value="z" selected="true">z_label</option>
... </param>
... '''))
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('argument', None), ('display', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', True)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', ['y', 'z'])]
>>> print(p.to_param_dict_string(["y", "z"]))
y,z

__init__(tool, input_source, context=None)

get_options(trans, other_values)

get_legal_values(trans, other_values)

from_json(value, trans, other_values={}, require_legal_value=True)

to_param_dict_string(value, other_values={})

to_json(value, app, use_security)

get_initial_value(trans, other_values)

to_text(value)

get_dependencies()

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

to_dict(trans, other_values={})

Submodules

galaxy.tools.parameters.basic module

Basic tool parameters.

galaxy.tools.parameters.basic.contains_workflow_parameter(value, search=False)

galaxy.tools.parameters.basic.is_runtime_value(value)

galaxy.tools.parameters.basic.is_runtime_context(trans, other_values)

galaxy.tools.parameters.basic.parse_dynamic_options(param, input_source)

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

Bases: galaxy.util.dictifiable.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, …)

dict_collection_visible_keys = ['name', 'argument', 'type', 'label', 'help', 'refresh_on_change']

__init__(tool, input_source, context=None)

visible

Return true if the parameter should be rendered on the form

get_label()

Return user friendly name for the parameter

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

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

get_initial_value(trans, other_values)

Return the starting value of 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)

get_dependencies()

Return the names of any other parameters this parameter depends on

to_json(value, app, use_security)

Convert a value to a string representation suitable for persisting

to_python(value, app)

Convert a value created with to_json back to an object representation

value_to_basic(value, app, use_security=False)

value_from_basic(value, app, ignore_errors=False)

value_to_display_text(value)

to_text(value)

Convert a value to a text representation suitable for displaying to the user >>> p = ToolParameter(None, XML(‘<param name=”_name” />’)) >>> print(p.to_text(None)) Not available. >>> print(p.to_text(‘’)) Empty. >>> print(p.to_text(‘text’)) text >>> print(p.to_text(True)) True >>> print(p.to_text(False)) False >>> print(p.to_text(0)) 0

to_param_dict_string(value, other_values={})

Called via __str__ when used in the Cheetah template

validate(value, trans=None)

to_dict(trans, other_values={})

to_dict tool parameter. This can be overridden by subclasses.

classmethod build(tool, param)

Factory method to create parameter of correct type

static parse_name(input_source)

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

Bases: galaxy.tools.parameters.basic.ToolParameter

Parameter that can take on any text value.

>>> from galaxy.util.bunch import Bunch
>>> trans = Bunch(app=None)
>>> p = TextToolParameter(None, XML('<param name="_name" type="text" value="default" />'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'TextToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'text'), ('value', u'default')]

__init__(tool, input_source)

to_json(value, app, use_security)

Convert a value to a string representation suitable for persisting

validate(value, trans=None)

get_initial_value(trans, other_values)

to_dict(trans, other_values={})

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

Bases: galaxy.tools.parameters.basic.TextToolParameter

Parameter that takes an integer value.

>>> from galaxy.util.bunch import Bunch
>>> trans = Bunch(app=None, history=Bunch(), workflow_building_mode=True)
>>> p = IntegerToolParameter(None, XML('<param name="_name" type="integer" value="10" />'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'IntegerToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'integer'), ('value', u'10')]
>>> assert type(p.from_json("10", trans)) == int
>>> type(p.from_json("_string", trans))
Traceback (most recent call last):
    ...
ValueError: An integer or workflow parameter e.g. ${name} is required

dict_collection_visible_keys = ['name', 'argument', 'type', 'label', 'help', 'refresh_on_change', 'min', 'max']

__init__(tool, input_source)

from_json(value, trans, other_values={})

to_python(value, app)

get_initial_value(trans, other_values)

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

Bases: galaxy.tools.parameters.basic.TextToolParameter

Parameter that takes a real number value.

>>> from galaxy.util.bunch import Bunch
>>> trans = Bunch(app=None, history=Bunch(), workflow_building_mode=True)
>>> p = FloatToolParameter(None, XML('<param name="_name" type="float" value="3.141592" />'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'FloatToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'float'), ('value', u'3.141592')]
>>> assert type(p.from_json("36.1", trans)) == float
>>> type(p.from_json("_string", trans))
Traceback (most recent call last):
    ...
ValueError: A real number or workflow parameter e.g. ${name} is required

dict_collection_visible_keys = ['name', 'argument', 'type', 'label', 'help', 'refresh_on_change', 'min', 'max']

__init__(tool, input_source)

from_json(value, trans, other_values={})

to_python(value, app)

get_initial_value(trans, other_values)

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

Bases: galaxy.tools.parameters.basic.ToolParameter

Parameter that takes one of two values.

>>> from galaxy.util.bunch import Bunch
>>> trans = Bunch(app=None, history=Bunch())
>>> p = BooleanToolParameter(None, XML('<param name="_name" type="boolean" checked="yes" truevalue="_truevalue" falsevalue="_falsevalue" />'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('falsevalue', '_falsevalue'), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'BooleanToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('truevalue', '_truevalue'), ('type', 'boolean'), ('value', 'true')]
>>> print(p.from_json('true'))
True
>>> print(p.to_param_dict_string(True))
_truevalue
>>> print(p.from_json('false'))
False
>>> print(p.to_param_dict_string(False))
_falsevalue

__init__(tool, input_source)

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

to_python(value, app=None)

to_json(value, app, use_security)

get_initial_value(trans, other_values)

to_param_dict_string(value, other_values={})

to_dict(trans, other_values={})

legal_values

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

Bases: galaxy.tools.parameters.basic.ToolParameter

Parameter that takes an uploaded file as a value.

>>> from galaxy.util.bunch import Bunch
>>> trans = Bunch(app=None, history=Bunch())
>>> p = FileToolParameter(None, XML('<param name="_name" type="file"/>'))
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FileToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'file'), ('value', None)]

__init__(tool, input_source)

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

get_required_enctype()

File upload elements require the multipart/form-data encoding

to_json(value, app, use_security)

to_python(value, app)

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 galaxy.util.bunch import Bunch
>>> trans = Bunch(app=None, history=Bunch(), user=None)
>>> p = FTPFileToolParameter(None, XML('<param name="_name" type="ftpfile"/>'))
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FTPFileToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'ftpfile'), ('value', None)]

__init__(tool, input_source)

get_initial_value(trans, other_values)

visible

to_param_dict_string(value, other_values={})

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

to_json(value, app, use_security)

to_python(value, app, validate=False)

to_dict(trans, other_values=None)

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

Bases: galaxy.tools.parameters.basic.ToolParameter

Parameter that takes one of two values.

__init__(tool, input_source)

get_initial_value(trans, other_values)

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

Bases: galaxy.tools.parameters.basic.ToolParameter

Parameter that takes one of two values.

>>> from galaxy.util.bunch import Bunch
>>> trans = Bunch(app=None, history=Bunch())
>>> p = HiddenToolParameter(None, XML('<param name="_name" type="hidden" value="_value"/>'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'HiddenToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'hidden'), ('value', u'_value')]

__init__(tool, input_source)

get_initial_value(trans, other_values)

get_label()

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

Bases: galaxy.tools.parameters.basic.ToolParameter

Parameter that stores a color.

>>> from galaxy.util.bunch import Bunch
>>> trans = Bunch(app=None, history=Bunch())
>>> p = ColorToolParameter(None, XML('<param name="_name" type="color" value="#ffffff"/>'))
>>> print(p.name)
_name
>>> print(p.to_param_dict_string("#fdeada"))
#fdeada
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ColorToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'color'), ('value', u'#ffffff')]
>>> p = ColorToolParameter(None, XML('<param name="_name" type="color" value="#ffffff" rgb="True"/>'))
>>> print(p.to_param_dict_string("#fdeada"))
(253, 234, 218)
>>> print(p.to_param_dict_string(None))
Traceback (most recent call last):
    ...
ValueError: Failed to convert 'None' to RGB.

__init__(tool, input_source)

get_initial_value(trans, other_values)

to_param_dict_string(value, other_values={})

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 galaxy.util.bunch import Bunch
>>> trans = Bunch(app=None, history=Bunch())
>>> p = BaseURLToolParameter(None, XML('<param name="_name" type="base_url" value="_value"/>'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'BaseURLToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'base_url'), ('value', u'_value')]

__init__(tool, input_source)

get_initial_value(trans, other_values)

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

to_dict(trans, other_values={})

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.

>>> from galaxy.util.bunch import Bunch
>>> trans = Bunch(app=None, history=Bunch(), workflow_building_mode=False)
>>> p = SelectToolParameter(None, XML(
... '''
... <param name="_name" type="select">
...     <option value="x">x_label</option>
...     <option value="y" selected="true">y_label</option>
...     <option value="z">z_label</option>
... </param>
... '''))
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('argument', None), ('display', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', False), ('name', '_name'), ('optional', False), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', False)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', 'y')]
>>> p = SelectToolParameter(None, XML(
... '''
... <param name="_name" type="select" multiple="true">
...     <option value="x">x_label</option>
...     <option value="y" selected="true">y_label</option>
...     <option value="z" selected="true">z_label</option>
... </param>
... '''))
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('argument', None), ('display', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', True)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', ['y', 'z'])]
>>> print(p.to_param_dict_string(["y", "z"]))
y,z

__init__(tool, input_source, context=None)

get_options(trans, other_values)

get_legal_values(trans, other_values)

from_json(value, trans, other_values={}, require_legal_value=True)

to_param_dict_string(value, other_values={})

to_json(value, app, use_security)

get_initial_value(trans, other_values)

to_text(value)

get_dependencies()

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

to_dict(trans, other_values={})

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(app=None, history=Bunch(genome_build='hg17'), db_builds=util.read_dbnames(None))
>>> p = GenomeBuildParameter(None, XML('<param name="_name" type="genomebuild" value="hg17" />'))
>>> print(p.name)
_name
>>> d = p.to_dict(trans)
>>> o = d['options']
>>> [i for i in o if i[2] == True]
[('Human May 2004 (NCBI35/hg17) (hg17)', 'hg17', True)]
>>> [i for i in o if i[1] == 'hg18']
[('Human Mar. 2006 (NCBI36/hg18) (hg18)', 'hg18', False)]

__init__(*args, **kwds)

get_options(trans, other_values)

get_legal_values(trans, other_values)

to_dict(trans, other_values={})

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

Bases: galaxy.tools.parameters.basic.SelectToolParameter

Select set that is composed of a set of tags available for an input.

__init__(tool, input_source)

from_json(value, trans, other_values={})

get_tag_list(other_values)

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

get_options(trans, other_values)

Show tags

get_initial_value(trans, other_values)

get_legal_values(trans, other_values)

get_dependencies()

to_dict(trans, other_values={})

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

__init__(tool, input_source)

from_json(value, trans, other_values={})

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_options(trans, other_values)

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

get_initial_value(trans, other_values)

get_legal_values(trans, other_values)

get_dependencies()

to_dict(trans, other_values={})

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.

>>> from galaxy.util.bunch import Bunch
>>> trans = Bunch(app=None, history=Bunch(genome_build='hg17'), db_builds=util.read_dbnames(None))
>>> p = DrillDownSelectToolParameter(None, XML(
... '''
... <param name="_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 2" value="heading2">
...          <option name="Option 3" value="option3"/>
...          <option name="Option 4" value="option4"/>
...        </option>
...    </option>
...    <option name="Option 5" value="option5"/>
...   </options>
... </param>
... '''))
>>> print(p.name)
_name
>>> d = p.to_dict(trans)
>>> assert d['multiple'] == True
>>> assert d['display'] == 'checkbox'
>>> assert d['options'][0]['name'] == 'Heading 1'
>>> assert d['options'][0]['value'] == 'heading1'
>>> assert d['options'][0]['options'][0]['name'] == 'Option 1'
>>> assert d['options'][0]['options'][0]['value'] == 'option1'
>>> assert d['options'][0]['options'][1]['name'] == 'Option 2'
>>> assert d['options'][0]['options'][1]['value'] == 'option2'
>>> assert d['options'][0]['options'][2]['name'] == 'Heading 2'
>>> assert d['options'][0]['options'][2]['value'] == 'heading2'
>>> assert d['options'][0]['options'][2]['options'][0]['name'] == 'Option 3'
>>> assert d['options'][0]['options'][2]['options'][0]['value'] == 'option3'
>>> assert d['options'][0]['options'][2]['options'][1]['name'] == 'Option 4'
>>> assert d['options'][0]['options'][2]['options'][1]['value'] == 'option4'
>>> assert d['options'][1]['name'] == 'Option 5'
>>> assert d['options'][1]['value'] == 'option5'

__init__(tool, input_source, context=None)

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

get_legal_values(trans, other_values)

from_json(value, trans, other_values={})

to_param_dict_string(value, other_values={})

get_initial_value(trans, other_values)

to_text(value)

get_dependencies()

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

to_dict(trans, other_values={})

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

Bases: galaxy.tools.parameters.basic.ToolParameter

__init__(tool, input_source, trans)

get_initial_value(trans, other_values)

to_json(value, app, use_security)

to_python(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.

__init__(tool, input_source, trans=None)

from_json(value, trans, other_values={})

to_param_dict_string(value, other_values={})

to_text(value)

validate(value, trans=None)

get_dependencies()

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

converter_safe(other_values, trans)

get_options_filter_attribute(value)

to_dict(trans, other_values={})

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

Bases: galaxy.tools.parameters.basic.BaseDataToolParameter

__init__(tool, input_source, trans=None)

collection_types

match_collections(trans, history, dataset_collection_matcher)

match_multirun_collections(trans, history, dataset_collection_matcher)

from_json(value, trans, other_values={})

to_text(value)

validate(value, trans=None)

to_dict(trans, other_values=None)

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.

__init__(tool, elem)

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

Bases: galaxy.tools.parameters.basic.ToolParameter

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

__init__(tool, input_source, context=None)

from_json(value, trans, other_values={})

to_param_dict_string(value, other_values={})

to_json(value, app, use_security)

to_python(value, app, other_values={}, validate=False)

to_dict(trans, other_values=None)

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

Bases: galaxy.tools.parameters.basic.ToolParameter

Class of parameter that tries to keep values as close to JSON as possible. In particular value_to_basic is overloaded to prevent params_to_strings from double encoding JSON and to_python using loads to produce values.

value_to_basic(value, app, use_security=False)

to_json(value, app, use_security)

Convert a value to a string representation suitable for persisting

to_python(value, app)

Convert a value created with to_json back to an object representation

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

Bases: galaxy.tools.parameters.basic.BaseJsonToolParameter

Parameter that allows for the creation of a list of rules using the Galaxy rules DSL.

__init__(tool, input_source, context=None)

to_dict(trans, other_values={})

validate(value, trans=None)

to_text(value)

galaxy.tools.parameters.basic.runtime_to_json(runtime_value)

galaxy.tools.parameters.basic.runtime_to_object(runtime_value)

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.ConnectedValue

Bases: galaxy.tools.parameters.basic.RuntimeValue

Wrapper to note a value that is not yet set, but will be inferred from a connection.

galaxy.tools.parameters.dataset_matcher module

galaxy.tools.parameters.dataset_matcher.set_dataset_matcher_factory(trans, tool)

galaxy.tools.parameters.dataset_matcher.unset_dataset_matcher_factory(trans)

galaxy.tools.parameters.dataset_matcher.get_dataset_matcher_factory(trans)

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

Bases: object

A filter takes the current options list and modifies it.

classmethod from_element(d_option, elem)

Loads the proper filter by the type attribute of elem

__init__(d_option, elem)

get_dependency_name()

Returns the name of any dependencies, otherwise None

filter_options(options, trans, other_values)

Returns a list of options after the filter is applied

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)

__init__(d_option, elem)

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 (,)

__init__(d_option, elem)

get_dependency_name()

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

__init__(d_option, elem)

get_dependency_name()

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

__init__(d_option, elem)

get_dependency_name()

filter_options(options, trans, other_values)

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 (,)

__init__(d_option, elem)

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 )

__init__(d_option, elem)

filter_options(options, trans, other_values)

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)

__init__(d_option, elem)

filter_options(options, trans, other_values)

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

__init__(d_option, elem)

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

__init__(d_option, elem)

filter_options(options, trans, other_values)

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

Bases: object

Handles dynamically generated SelectToolParameter options

__init__(elem, tool_param)

tool_data_table

missing_tool_data_table_name

parse_column_definitions(elem)

parse_file_fields(reader)

get_dependency_names()

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

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_field_by_name_for_value(field_name, value, trans, other_values)

Get contents of field by name for specified value.

get_options(trans, other_values)

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.

galaxy.tools.parameters.grouping module

Constructs for grouping tool parameters

class galaxy.tools.parameters.grouping.Group

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['name', 'type']

__init__()

visible

value_to_basic(value, app)

Convert value to a (possibly nested) representation using only basic types (dict, list, tuple, string_types, int, long, float, bool, 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.

get_initial_value(trans, context)

Return the initial state/value for this group

to_dict(trans)

class galaxy.tools.parameters.grouping.Repeat

Bases: galaxy.tools.parameters.grouping.Group

dict_collection_visible_keys = ['name', 'type', 'title', 'help', 'default', 'min', 'max']

type = 'repeat'

__init__()

title_plural

label()

value_to_basic(value, app)

value_from_basic(value, app, ignore_errors=False)

get_initial_value(trans, context)

to_dict(trans)

class galaxy.tools.parameters.grouping.Section

Bases: galaxy.tools.parameters.grouping.Group

dict_collection_visible_keys = ['name', 'type', 'title', 'help', 'expanded']

type = 'section'

__init__()

title_plural

label()

value_to_basic(value, app)

value_from_basic(value, app, ignore_errors=False)

get_initial_value(trans, context)

to_dict(trans)

class galaxy.tools.parameters.grouping.UploadDataset

Bases: galaxy.tools.parameters.grouping.Group

type = 'upload_dataset'

__init__()

get_composite_dataset_name(context)

get_file_base_name(context)

get_file_type(context, parent_context=None)

get_dbkey(context, parent_context=None)

get_datatype_ext(trans, context, parent_context=None)

get_datatype(trans, context, parent_context=None)

title_plural

group_title(context)

title_by_index(trans, index, context)

value_to_basic(value, app)

value_from_basic(value, app, ignore_errors=False)

get_file_count(trans, context)

get_initial_value(trans, context)

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

class galaxy.tools.parameters.grouping.Conditional

Bases: galaxy.tools.parameters.grouping.Group

type = 'conditional'

__init__()

label

get_current_case(value)

value_to_basic(value, app)

value_from_basic(value, app, ignore_errors=False)

get_initial_value(trans, context)

to_dict(trans)

class galaxy.tools.parameters.grouping.ConditionalWhen

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['value']

__init__()

to_dict(trans)

galaxy.tools.parameters.history_query module

class galaxy.tools.parameters.history_query.HistoryQuery(**kwargs)

Bases: object

An object for describing the collections to pull out of a history, used by DataCollectionToolParameter.

__init__(**kwargs)

static from_collection_type(collection_type, collection_type_descriptions)

static from_collection_types(collection_types, collection_type_descriptions)

static from_parameter(param, collection_type_descriptions)

Take in a tool parameter element.

direct_match(hdca)

can_map_over(hdca)

galaxy.tools.parameters.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(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

__init__()

translate(params)

update params in-place

galaxy.tools.parameters.meta module

galaxy.tools.parameters.meta.expand_workflow_inputs(inputs)

Expands incoming encoded multiple payloads, into the set of all individual payload combinations >>> params, param_keys = expand_workflow_inputs({‘1’: {‘input’: {‘batch’: True, ‘product’: True, ‘values’: [{‘hid’: ‘1’}, {‘hid’: ‘2’}] }}}) >>> print([“%s” % (p[‘1’][‘input’][‘hid’]) for p in params]) [‘1’, ‘2’] >>> params, param_keys = expand_workflow_inputs({‘1’: {‘input’: {‘batch’: True, ‘values’: [{‘hid’: ‘1’}, {‘hid’: ‘2’}] }}}) >>> print([“%s” % (p[‘1’][‘input’][‘hid’]) for p in params]) [‘1’, ‘2’] >>> params, param_keys = expand_workflow_inputs({‘1’: {‘input’: {‘batch’: True, ‘values’: [{‘hid’: ‘1’}, {‘hid’: ‘2’}] }}, ‘2’: {‘input’: {‘batch’: True, ‘values’: [{‘hid’: ‘3’}, {‘hid’: ‘4’}] }}}) >>> print([“%s%s” % (p[‘1’][‘input’][‘hid’], p[‘2’][‘input’][‘hid’]) for p in params]) [‘13’, ‘24’] >>> params, param_keys = expand_workflow_inputs({‘1’: {‘input’: {‘batch’: True, ‘product’: True, ‘values’: [{‘hid’: ‘1’}, {‘hid’: ‘2’}] }}, ‘2’: {‘input’: {‘batch’: True, ‘values’: [{‘hid’: ‘3’}, {‘hid’: ‘4’}, {‘hid’: ‘5’}] }}}) >>> print([“%s%s” % (p[‘1’][‘input’][‘hid’], p[‘2’][‘input’][‘hid’]) for p in params]) [‘13’, ‘23’, ‘14’, ‘24’, ‘15’, ‘25’] >>> params, param_keys = expand_workflow_inputs({‘1’: {‘input’: {‘batch’: True, ‘product’: True, ‘values’: [{‘hid’: ‘1’}, {‘hid’: ‘2’}] }}, ‘2’: {‘input’: {‘batch’: True, ‘product’: True, ‘values’: [{‘hid’: ‘3’}, {‘hid’: ‘4’}, {‘hid’: ‘5’}] }}, ‘3’: {‘input’: {‘batch’: True, ‘product’: True, ‘values’: [{‘hid’: ‘6’}, {‘hid’: ‘7’}, {‘hid’: ‘8’}] }}}) >>> print([“%s%s%s” % (p[‘1’][‘input’][‘hid’], p[‘2’][‘input’][‘hid’], p[‘3’][‘input’][‘hid’]) for p in params]) [‘136’, ‘137’, ‘138’, ‘146’, ‘147’, ‘148’, ‘156’, ‘157’, ‘158’, ‘236’, ‘237’, ‘238’, ‘246’, ‘247’, ‘248’, ‘256’, ‘257’, ‘258’]

galaxy.tools.parameters.meta.process_key(incoming_key, incoming_value, d)

galaxy.tools.parameters.meta.expand_meta_parameters(trans, tool, incoming)

Take in a dictionary of raw incoming parameters and expand to a list of expanded incoming parameters (one set of parameters per tool execution).

galaxy.tools.parameters.output_collect module

Code allowing tools to define extra files associated with an output datset.

class galaxy.tools.parameters.output_collect.NullToolProvidedMetadata

Bases: object

get_new_datasets(output_name)

get_new_dataset_meta_by_basename(output_name, basename)

has_failed_outputs()

get_unnamed_outputs()

class galaxy.tools.parameters.output_collect.LegacyToolProvidedMetadata(job_wrapper, meta_file)

Bases: object

__init__(job_wrapper, meta_file)

get_meta_by_dataset_id(dataset_id)

get_new_dataset_meta_by_basename(output_name, basename)

get_new_datasets(output_name)

has_failed_outputs()

get_unnamed_outputs()

class galaxy.tools.parameters.output_collect.ToolProvidedMetadata(job_wrapper, meta_file)

Bases: object

__init__(job_wrapper, meta_file)

get_meta_by_name(name)

get_new_dataset_meta_by_basename(output_name, basename)

get_new_datasets(output_name)

has_failed_outputs()

get_unnamed_outputs()

galaxy.tools.parameters.output_collect.collect_dynamic_outputs(tool, output_collections, tool_provided_metadata, job_working_directory, inp_data={}, job=None, input_dbkey='?')

class galaxy.tools.parameters.output_collect.JobContext(tool, tool_provided_metadata, job, job_working_directory, inp_data, input_dbkey)

Bases: object

__init__(tool, tool_provided_metadata, job, job_working_directory, inp_data, input_dbkey)

work_context

permissions

find_files(output_name, collection, dataset_collectors)

populate_collection_elements(collection, root_collection_builder, filenames, name=None, metadata_source_name=None)

create_dataset(ext, designation, visible, dbkey, name, filename, metadata_source_name=None, info=None, library_folder=None, link_data=False, primary_data=None, tag_list=[])

galaxy.tools.parameters.output_collect.collect_primary_datasets(tool, output, tool_provided_metadata, job_working_directory, input_ext, input_dbkey='?')

class galaxy.tools.parameters.output_collect.DiscoveredFile(path, collector, match)

Bases: tuple

collector

Alias for field number 1

match

Alias for field number 2

path

Alias for field number 0

galaxy.tools.parameters.output_collect.discover_files(output_name, tool_provided_metadata, extra_file_collectors, job_working_directory, matchable)

galaxy.tools.parameters.output_collect.discovered_file_for_unnamed_output(dataset, job_working_directory, parent_identifiers=[])

galaxy.tools.parameters.output_collect.discover_target_directory(dir_name, job_working_directory)

galaxy.tools.parameters.output_collect.walk_over_file_collectors(extra_file_collectors, job_working_directory, matchable)

galaxy.tools.parameters.output_collect.walk_over_extra_files(target_dir, extra_file_collector, job_working_directory, matchable)

Walks through all files in a given directory, and returns all files that match the given collector’s match criteria. If the collector has the recurse flag enabled, will also recursively descend into child folders.

galaxy.tools.parameters.output_collect.dataset_collector(dataset_collection_description)

class galaxy.tools.parameters.output_collect.ToolMetadataDatasetCollector(dataset_collection_description)

Bases: object

__init__(dataset_collection_description)

class galaxy.tools.parameters.output_collect.DatasetCollector(dataset_collection_description)

Bases: object

__init__(dataset_collection_description)

match(dataset_instance, filename, path=None)

sort(matches)

class galaxy.tools.parameters.output_collect.JsonCollectedDatasetMatch(as_dict, collector, filename, path=None, parent_identifiers=[])

Bases: object

__init__(as_dict, collector, filename, path=None, parent_identifiers=[])

designation

element_identifiers

raw_element_identifiers

name

Return name or None if not defined by the discovery pattern.

dbkey

ext

visible

link_data

tag_list

object_id

class galaxy.tools.parameters.output_collect.RegexCollectedDatasetMatch(re_match, collector, filename, path=None)

Bases: galaxy.tools.parameters.output_collect.JsonCollectedDatasetMatch

__init__(re_match, collector, filename, path=None)

galaxy.tools.parameters.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.ascii_letters"/>
... </sanitizer>
... '''))
>>> sanitizer.sanitize_param(''.join(sorted(c for c in string.printable))) == ''.join(sorted(c for c in string.ascii_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

VALID_PRESET = {'default': 'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789 -=_.()/+*^,:?!', 'none': ''}

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

DEFAULT_INVALID_CHAR = 'X'

classmethod from_element(elem)

Loads the proper filter by the type attribute of elem

classmethod get_valid_by_name(name)

classmethod get_mapping_by_name(name)

__init__()

restore_text(text)

Restores sanitized text

sanitize_text(text)

Restricts the characters that are allowed in a text

sanitize_param(value)

Clean incoming parameters (strings or lists)

galaxy.tools.parameters.validation module

Classes related to parameter validation.

class galaxy.tools.parameters.validation.Validator

Bases: object

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

requires_dataset_metadata = False

classmethod from_element(param, elem)

validate(value, trans=None)

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

Bases: galaxy.tools.parameters.validation.Validator

Validator that evaluates a regular expression

>>> from xml.etree.ElementTree import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="text" 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)

__init__(message, expression)

validate(value, trans=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 xml.etree.ElementTree import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="text" 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)

__init__(message, expression, substitute_value_in_message)

validate(value, trans=None)

class galaxy.tools.parameters.validation.InRangeValidator(message, range_min, range_max, exclude_min=False, exclude_max=False)

Bases: galaxy.tools.parameters.validation.Validator

Validator that ensures a number is in a specific range

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

__init__(message, range_min, range_max, exclude_min=False, exclude_max=False)

When the optional exclude_min and exclude_max attributes are set to true, the range excludes the end points (i.e., min < value < max), while if set to False (the default), then range includes the end points (1.e., min <= value <= max). Combinations of exclude_min and exclude_max values are allowed.

validate(value, trans=None)

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 xml.etree.ElementTree import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="text" 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)

__init__(message, length_min, length_max)

validate(value, trans=None)

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

__init__(message=None)

classmethod from_element(param, elem)

validate(value, trans=None)

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

Bases: galaxy.tools.parameters.validation.Validator

Validator that checks if a dataset has a positive file size.

__init__(message=None)

classmethod from_element(param, elem)

validate(value, trans=None)

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

Bases: galaxy.tools.parameters.validation.Validator

Validator that checks if a dataset’s extra_files_path exists and is not empty.

__init__(message=None)

classmethod from_element(param, elem)

validate(value, trans=None)

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

Bases: galaxy.tools.parameters.validation.Validator

Validator that checks for missing metadata

requires_dataset_metadata = True

__init__(message=None, check='', skip='')

classmethod from_element(param, elem)

validate(value, trans=None)

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

Bases: galaxy.tools.parameters.validation.Validator

Validator that checks for dbkey not equal to ‘?’

requires_dataset_metadata = True

__init__(message=None)

classmethod from_element(param, elem)

validate(value, trans=None)

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

Bases: galaxy.tools.parameters.validation.Validator

Validator that checks for empty select list

__init__(message=None)

classmethod from_element(param, elem)

validate(value, trans=None)

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

Bases: galaxy.tools.parameters.validation.Validator

Validator that checks for empty text field

__init__(message=None)

classmethod from_element(param, elem)

validate(value, trans=None)

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

Bases: galaxy.tools.parameters.validation.Validator

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

requires_dataset_metadata = True

classmethod from_element(param, elem)

__init__(filename, metadata_name, metadata_column, message='Value for metadata not found.', line_startswith=None, split='\t')

validate(value, trans=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.

requires_dataset_metadata = True

classmethod from_element(param, elem)

__init__(tool_data_table, metadata_name, metadata_column, message='Value for metadata not found.', line_startswith=None)

validate(value, trans=None)

galaxy.tools.parameters.validation.get_suite()

Get unittest suite for this module

galaxy.tools.parameters.wrapped module

class galaxy.tools.parameters.wrapped.WrappedParameters(trans, tool, incoming, input_datasets=None)

Bases: object

__init__(trans, tool, incoming, input_datasets=None)

params

wrap_values(inputs, input_values, skip_missing_values=False)

galaxy.tools.parameters.wrapped.make_dict_copy(from_dict)

Makes a copy of input dictionary from_dict such that all values that are dictionaries result in creation of a new dictionary ( a sort of deepcopy ). We may need to handle other complex types ( e.g., lists, etc ), but not sure… Yes, we need to handle lists (and now are)…

galaxy.tools.parameters.wrapped_json module

galaxy.tools.parameters.wrapped_json.json_wrap(inputs, input_values, as_dict=None, handle_files='skip')