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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.

exception galaxy.tools.parameters.basic.ImplicitConversionRequired

Bases: Exception

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, …)

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

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, input_source)

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: parameter '_name': an integer or workflow parameter 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: parameter '_name': an integer or workflow parameter 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.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("#ffffff"))
#ffffff
>>> 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"/>'))
>>> print(p.get_initial_value(trans, {}))
#000000
>>> p = ColorToolParameter(None, XML('<param name="_name" type="color" value="#ffffff" rgb="True"/>'))
>>> print(p.to_param_dict_string("#ffffff"))
(255, 255, 255)
>>> 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.RegexpFilter(d_option, elem)

Bases: galaxy.tools.parameters.dynamic_options.Filter

Filters a list of options on a column by a regular expression.

Type: regexp

Required Attributes:

value: regular expression to compare to column: column in options to compare with

Optional Attributes:

keep: Keep columns matching the regexp (True)

Discard columns matching the regexp (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.

DEPRECATED: just replace with 2 rounds of MultipleSplitterFilter

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

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, 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.sanitize module

Tool Parameter specific sanitizing.

class galaxy.tools.parameters.sanitize.ToolParameterSanitizer

Bases: object

Handles tool parameter specific sanitizing.

>>> from galaxy.util 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': {'>': '__gt__', '<': '__lt__', "'": '__sq__', '"': '__dq__', '[': '__ob__', ']': '__cb__', '{': '__oc__', '}': '__cc__', '@': '__at__', '\n': '__cn__', '\r': '__cr__', '\t': '__tc__', '#': '__pd__'}, '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)

Initialize the appropiate Validator class

example call validation.Validator.from_element(ToolParameter_object, Validator_object)

needs to be implemented in the subclasses and should return the corresponding Validator object by a call to cls( … ) which calls the __init__ method of the corresponding validator

param cls the Validator class param param the element to be evaluated (which contains the validator) param elem the validator element return an object of a Validator subclass that corresponds to the type attribute of the validator element

validate(value, trans=None)

validate a value

return None if positive validation, otherwise a ValueError is raised

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

Bases: galaxy.tools.parameters.validation.Validator

Validator that evaluates a regular expression

>>> from galaxy.util 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
>>> t = p.validate(["Foo", "foo"])
>>> t = p.validate(["Foo", "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 galaxy.util 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 specified range

>>> from galaxy.util 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 galaxy.util 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.ValueInDataTableColumnValidator(tool_data_table, column, message='Value not found.', line_startswith=None)

Bases: galaxy.tools.parameters.validation.Validator

Validator that checks if a value is in a tool data table column.

classmethod from_element(param, elem)

__init__(tool_data_table, column, message='Value not found.', line_startswith=None)

validate(value, trans=None)

class galaxy.tools.parameters.validation.ValueNotInDataTableColumnValidator(tool_data_table, metadata_column, message='Value already present.', line_startswith=None)

Bases: galaxy.tools.parameters.validation.ValueInDataTableColumnValidator

Validator that checks if a value is NOT in a tool data table column.

__init__(tool_data_table, metadata_column, message='Value already present.', line_startswith=None)

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)

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

Bases: galaxy.tools.parameters.validation.MetadataInDataTableColumnValidator

Validator that checks if the value for a dataset’s metadata item doesn’t exists in a file.

requires_dataset_metadata = True

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

validate(value, trans=None)

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

Bases: galaxy.tools.parameters.validation.InRangeValidator

Validator that ensures metadata is in a specified range

requires_dataset_metadata = True

classmethod from_element(param, elem)

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

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, profile, as_dict=None, handle_files='skip')