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galaxy.tools package

Classes encapsulating galaxy tools and tool configuration.

class galaxy.tools.ToolErrorLog

Bases: object

__init__()

add_error(file, phase, exception)

exception galaxy.tools.ToolInputsNotReadyException

Bases: exceptions.Exception

exception galaxy.tools.ToolNotFoundException

Bases: exceptions.Exception

galaxy.tools.create_tool_from_source(app, tool_source, config_file=None, **kwds)

class galaxy.tools.ToolBox(config_filenames, tool_root_dir, app)

Bases: galaxy.tools.toolbox.base.BaseGalaxyToolBox

A derivative of AbstractToolBox with knowledge about Tool internals - how to construct them, action types, dependency management, etc….

__init__(config_filenames, tool_root_dir, app)

handle_panel_update(section_dict)

Sends a panel update to all threads/processes.

has_reloaded(other_toolbox)

all_requirements

tools_by_id

create_tool(config_file, **kwds)

create_dynamic_tool(dynamic_tool, **kwds)

get_tool_components(tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=False)

Retrieve all loaded versions of a tool from the toolbox and return a select list enabling selection of a different version, the list of the tool’s loaded versions, and the specified tool.

class galaxy.tools.DefaultToolState

Bases: object

Keeps track of the state of a users interaction with a tool between requests.

__init__()

initialize(trans, tool)

Create a new DefaultToolState for this tool. It will be initialized with default values for inputs. Grouping elements are filled in recursively.

encode(tool, app, nested=False)

Convert the data to a string

decode(values, tool, app)

Restore the state from a string

copy()

Shallow copy of the state

class galaxy.tools.Tool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.util.dictifiable.Dictifiable

Represents a computational tool that can be executed through Galaxy.

tool_type = 'default'

requires_setting_metadata = True

default_tool_action

alias of galaxy.tools.actions.DefaultToolAction

dict_collection_visible_keys = ['id', 'name', 'version', 'description', 'labels']

__init__(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Load a tool from the config named by config_file

history_manager

version_object

sa_session

Returns a SQLAlchemy session

lineage

Return ToolLineage for this tool.

tool_versions

tool_shed_repository

produces_collections_with_unknown_structure

valid_input_states

requires_galaxy_python_environment

Indicates this tool’s runtime requires Galaxy’s Python environment.

get_configured_job_handler(job_params=None)

Get the configured job handler for this Tool given the provided job_params.

Unlike the former get_job_handler() method, this does not perform “preassignment” (random selection of a configured handler ID from a tag).

Parameters:job_params (dict or None) – Any params specific to this job (e.g. the job source) Returns:str or None – The configured handler for a job run of this Tool

get_job_destination(job_params=None)

Returns:galaxy.jobs.JobDestination – The destination definition and runner parameters.

get_panel_section()

allow_user_access(user, attempting_access=True)

Returns:bool – Whether the user is allowed to access the tool.

parse(tool_source, guid=None, dynamic=False)

Read tool configuration from the element root and fill in self.

tests

test_data_path(filename)

tool_provided_metadata(job_wrapper)

parse_command(tool_source)

parse_environment_variables(tool_source)

parse_inputs(tool_source)

Parse the “<inputs>” element and create appropriate `ToolParameter`s. This implementation supports multiple pages and grouping constructs.

parse_help(tool_source)

Parse the help text for the tool. Formatted in reStructuredText, but stored as Mako to allow for dynamic image paths. This implementation supports multiple pages.

parse_outputs(tool_source)

Parse <outputs> elements and fill in self.outputs (keyed by name)

parse_stdio(tool_source)

Parse <stdio> element(s) and fill in self.return_codes, self.stderr_rules, and self.stdout_rules. Return codes have a range and an error type (fault or warning). Stderr and stdout rules have a regular expression and an error level (fault or warning).

parse_input_elem(page_source, enctypes, context=None)

Parse a parent element whose children are inputs – these could be groups (repeat, conditional) or param elements. Groups will be parsed recursively.

parse_param_elem(input_source, enctypes, context)

Parse a single “<param>” element and return a ToolParameter instance. Also, if the parameter has a ‘required_enctype’ add it to the set enctypes.

populate_resource_parameters(tool_source)

populate_tool_shed_info(tool_shed_repository)

help

help_by_page

raw_help

find_output_def(name)

check_workflow_compatible(tool_source)

Determine if a tool can be used in workflows. External tools and the upload tool are currently not supported by workflows.

new_state(trans)

Create a new DefaultToolState for this tool. It will be initialized with default values for inputs. Grouping elements are filled in recursively.

get_param(key)

Returns the parameter named key or None if there is no such parameter.

get_hook(name)

Returns an object from the code file referenced by code_namespace (this will normally be a callable object)

visit_inputs(values, callback)

Call the function callback on each parameter of this tool. Visits grouping parameters recursively and constructs unique prefixes for each nested set of The callback method is then called as:

callback( level_prefix, parameter, parameter_value )

expand_incoming(trans, incoming, request_context)

handle_input(trans, incoming, history=None, use_cached_job=False)

Process incoming parameters for this tool from the dict incoming, update the tool state (or create if none existed), and either return to the form or execute the tool (only if ‘execute’ was clicked and there were no errors).

handle_single_execution(trans, rerun_remap_job_id, execution_slice, history, execution_cache=None, completed_job=None, collection_info=None)

Return a pair with whether execution is successful as well as either resulting output data or an error message indicating the problem.

find_fieldstorage(x)

params_with_missing_data_table_entry

Return all parameters that are dynamically generated select lists whose options require an entry not currently in the tool_data_table_conf.xml file.

params_with_missing_index_file

Return all parameters that are dynamically generated select lists whose options refer to a missing .loc file.

get_static_param_values(trans)

Returns a map of parameter names and values if the tool does not require any user input. Will raise an exception if any parameter does require input.

execute(trans, incoming={}, set_output_hid=True, history=None, **kwargs)

Execute the tool using parameter values in incoming. This just dispatches to the ToolAction instance specified by self.tool_action. In general this will create a Job that when run will build the tool’s outputs, e.g. DefaultToolAction.

params_to_strings(params, app, nested=False)

params_from_strings(params, app, ignore_errors=False)

check_and_update_param_values(values, trans, update_values=True, workflow_building_mode=False)

Check that all parameters have values, and fill in with default values where necessary. This could be called after loading values from a database in case new parameters have been added.

build_dependency_cache(**kwds)

build_dependency_shell_commands(job_directory=None, metadata=False)

Return a list of commands to be run to populate the current environment to include this tools requirements.

installed_tool_dependencies

tool_requirements

Return all requiremens of type package

tool_requirements_status

Return a list of dictionaries for all tool dependencies with their associated status

build_redirect_url_params(param_dict)

Substitute parameter values into self.redirect_url_params

parse_redirect_url(data, param_dict)

Parse the REDIRECT_URL tool param. Tools that send data to an external application via a redirect must include the following 3 tool params:

1. REDIRECT_URL - the url to which the data is being sent
2. DATA_URL - the url to which the receiving application will send an http post to retrieve the Galaxy data
3. GALAXY_URL - the url to which the external application may post data as a response

call_hook(hook_name, *args, **kwargs)

Call the custom code hook function identified by ‘hook_name’ if any, and return the results

exec_before_job(app, inp_data, out_data, param_dict={})

exec_after_process(app, inp_data, out_data, param_dict, job=None)

job_failed(job_wrapper, message, exception=False)

Called when a job has failed

discover_outputs(out_data, out_collections, tool_provided_metadata, tool_working_directory, job, input_ext, input_dbkey, inp_data=None)

Find any additional datasets generated by a tool and attach (for cases where number of outputs is not known in advance).

to_archive()

to_dict(trans, link_details=False, io_details=False)

Returns dict of tool.

to_json(trans, kwd={}, job=None, workflow_building_mode=False)

Recursively creates a tool dictionary containing repeats, dynamic options and updated states.

populate_model(request_context, inputs, state_inputs, group_inputs, other_values=None)

Populates the tool model consumed by the client form builder.

get_default_history_by_trans(trans, create=False)

classmethod get_externally_referenced_paths(path)

Return relative paths to externally referenced files by the tool described by file at path. External components should not assume things about the structure of tool xml files (this is the tool’s responsibility).

class galaxy.tools.OutputParameterJSONTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.Tool

Alternate implementation of Tool that provides parameters and other values JSONified within the contents of an output dataset

tool_type = 'output_parameter_json'

exec_before_job(app, inp_data, out_data, param_dict=None)

class galaxy.tools.ExpressionTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.Tool

requires_js_runtime = True

tool_type = 'expression'

EXPRESSION_INPUTS_NAME = '_expression_inputs_.json'

parse_command(tool_source)

parse_outputs(tool_source)

exec_before_job(app, inp_data, out_data, param_dict=None)

parse_environment_variables(tool_source)

Setup environment variable for inputs file.

class galaxy.tools.DataSourceTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.OutputParameterJSONTool

Alternate implementation of Tool for data_source tools – those that allow the user to query and extract data from another web site.

tool_type = 'data_source'

default_tool_action

alias of galaxy.tools.actions.data_source.DataSourceToolAction

parse_inputs(tool_source)

exec_before_job(app, inp_data, out_data, param_dict=None)

class galaxy.tools.AsyncDataSourceTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.DataSourceTool

tool_type = 'data_source_async'

class galaxy.tools.DataDestinationTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.Tool

tool_type = 'data_destination'

class galaxy.tools.SetMetadataTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.Tool

Tool implementation for special tool that sets metadata on an existing dataset.

tool_type = 'set_metadata'

requires_setting_metadata = False

regenerate_imported_metadata_if_needed(hda, history, job)

exec_after_process(app, inp_data, out_data, param_dict, job=None)

job_failed(job_wrapper, message, exception=False)

class galaxy.tools.ExportHistoryTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.Tool

tool_type = 'export_history'

class galaxy.tools.ImportHistoryTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.Tool

tool_type = 'import_history'

class galaxy.tools.DataManagerTool(config_file, root, app, guid=None, data_manager_id=None, **kwds)

Bases: galaxy.tools.OutputParameterJSONTool

tool_type = 'manage_data'

default_tool_action

alias of galaxy.tools.actions.data_manager.DataManagerToolAction

__init__(config_file, root, app, guid=None, data_manager_id=None, **kwds)

exec_after_process(app, inp_data, out_data, param_dict, job=None, **kwds)

get_default_history_by_trans(trans, create=False)

allow_user_access(user, attempting_access=True)

Parameters:

• user (galaxy.model.User) – model object representing user.
• attempting_access (bool) – is the user attempting to do something with the the tool (set false for incidental checks like toolbox listing)

Returns:

bool – Whether the user is allowed to access the tool.

Data Manager tools are only accessible to admins.

class galaxy.tools.DatabaseOperationTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.Tool

default_tool_action

alias of galaxy.tools.actions.model_operations.ModelOperationToolAction

require_dataset_ok = True

valid_input_states

allow_errored_inputs

check_inputs_ready(input_datasets, input_dataset_collections)

produce_outputs(trans, out_data, output_collections, incoming, history)

class galaxy.tools.UnzipCollectionTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.DatabaseOperationTool

tool_type = 'unzip_collection'

produce_outputs(trans, out_data, output_collections, incoming, history, tags=None)

class galaxy.tools.ZipCollectionTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.DatabaseOperationTool

tool_type = 'zip_collection'

produce_outputs(trans, out_data, output_collections, incoming, history, **kwds)

class galaxy.tools.BuildListCollectionTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.DatabaseOperationTool

tool_type = 'build_list'

produce_outputs(trans, out_data, output_collections, incoming, history, tags=None)

class galaxy.tools.ExtractDatasetCollectionTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.DatabaseOperationTool

tool_type = 'extract_dataset'

produce_outputs(trans, out_data, output_collections, incoming, history, tags=None)

class galaxy.tools.MergeCollectionTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.DatabaseOperationTool

tool_type = 'merge_collection'

produce_outputs(trans, out_data, output_collections, incoming, history, **kwds)

class galaxy.tools.FilterDatasetsTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.DatabaseOperationTool

produce_outputs(trans, out_data, output_collections, incoming, history, **kwds)

class galaxy.tools.FilterFailedDatasetsTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.FilterDatasetsTool

tool_type = 'filter_failed_datasets_collection'

require_dataset_ok = False

element_is_valid(element)

class galaxy.tools.FilterEmptyDatasetsTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.FilterDatasetsTool

tool_type = 'filter_empty_datasets_collection'

require_dataset_ok = False

element_is_valid(element)

class galaxy.tools.FlattenTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.DatabaseOperationTool

tool_type = 'flatten_collection'

produce_outputs(trans, out_data, output_collections, incoming, history, **kwds)

class galaxy.tools.SortTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.DatabaseOperationTool

tool_type = 'sort_collection'

produce_outputs(trans, out_data, output_collections, incoming, history, **kwds)

class galaxy.tools.RelabelFromFileTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.DatabaseOperationTool

tool_type = 'relabel_from_file'

produce_outputs(trans, out_data, output_collections, incoming, history, **kwds)

class galaxy.tools.ApplyRulesTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.DatabaseOperationTool

tool_type = 'apply_rules'

produce_outputs(trans, out_data, output_collections, incoming, history, **kwds)

class galaxy.tools.TagFromFileTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.DatabaseOperationTool

tool_type = 'tag_from_file'

produce_outputs(trans, out_data, output_collections, incoming, history, **kwds)

class galaxy.tools.FilterFromFileTool(config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False)

Bases: galaxy.tools.DatabaseOperationTool

tool_type = 'filter_from_file'

produce_outputs(trans, out_data, output_collections, incoming, history, **kwds)

class galaxy.tools.TracksterConfig(actions)

Bases: object

Trackster configuration encapsulation.

__init__(actions)

static parse(root)

class galaxy.tools.SetParamAction(name, output_name)

Bases: object

Set parameter action.

__init__(name, output_name)

static parse(elt)

Parse action from element.

class galaxy.tools.BadValue(value)

Bases: object

__init__(value)

galaxy.tools.tool_class

alias of galaxy.tools.DataDestinationTool

exception galaxy.tools.InterruptedUpload

Bases: exceptions.Exception

Subpackages

• galaxy.tools.actions package
  • Submodules
  • galaxy.tools.actions.data_manager module
  • galaxy.tools.actions.data_source module
  • galaxy.tools.actions.history_imp_exp module
  • galaxy.tools.actions.metadata module
  • galaxy.tools.actions.model_operations module
  • galaxy.tools.actions.upload module
  • galaxy.tools.actions.upload_common module
• galaxy.tools.cwl package
  • Submodules
  • galaxy.tools.cwl.cwltool_deps module
  • galaxy.tools.cwl.parser module
  • galaxy.tools.cwl.representation module
  • galaxy.tools.cwl.runtime_actions module
  • galaxy.tools.cwl.schema module
  • galaxy.tools.cwl.util module
• galaxy.tools.data package
• galaxy.tools.data_manager package
  • Submodules
  • galaxy.tools.data_manager.manager module
• galaxy.tools.deps package
  • Subpackages
    • galaxy.tools.deps.container_resolvers package
      • Submodules
      • galaxy.tools.deps.container_resolvers.explicit module
      • galaxy.tools.deps.container_resolvers.mulled module
    • galaxy.tools.deps.mulled package
      • Submodules
      • galaxy.tools.deps.mulled.mulled_build module
      • galaxy.tools.deps.mulled.mulled_build_channel module
      • galaxy.tools.deps.mulled.mulled_build_files module
      • galaxy.tools.deps.mulled.mulled_build_tool module
      • galaxy.tools.deps.mulled.mulled_search module
      • galaxy.tools.deps.mulled.util module
    • galaxy.tools.deps.resolvers package
      • Submodules
      • galaxy.tools.deps.resolvers.brewed_tool_shed_packages module
      • galaxy.tools.deps.resolvers.conda module
      • galaxy.tools.deps.resolvers.galaxy_packages module
      • galaxy.tools.deps.resolvers.homebrew module
      • galaxy.tools.deps.resolvers.lmod module
      • galaxy.tools.deps.resolvers.modules module
      • galaxy.tools.deps.resolvers.resolver_mixins module
      • galaxy.tools.deps.resolvers.tool_shed_packages module
      • galaxy.tools.deps.resolvers.unlinked_tool_shed_packages module
  • Submodules
  • galaxy.tools.deps.brew_exts module
  • galaxy.tools.deps.brew_util module
  • galaxy.tools.deps.commands module
  • galaxy.tools.deps.conda_compat module
  • galaxy.tools.deps.conda_util module
  • galaxy.tools.deps.container_classes module
  • galaxy.tools.deps.containers module
  • galaxy.tools.deps.dependencies module
  • galaxy.tools.deps.docker_util module
  • galaxy.tools.deps.dockerfiles module
  • galaxy.tools.deps.installable module
  • galaxy.tools.deps.requirements module
  • galaxy.tools.deps.singularity_util module
  • galaxy.tools.deps.views module
• galaxy.tools.error_reports package
  • Subpackages
    • galaxy.tools.error_reports.plugins package
      • Submodules
      • galaxy.tools.error_reports.plugins.biostars module
      • galaxy.tools.error_reports.plugins.email module
      • galaxy.tools.error_reports.plugins.github module
      • galaxy.tools.error_reports.plugins.influxdb module
      • galaxy.tools.error_reports.plugins.json module
      • galaxy.tools.error_reports.plugins.sentry module
• galaxy.tools.filters package
• galaxy.tools.imp_exp package
  • Submodules
  • galaxy.tools.imp_exp.export_history module
  • galaxy.tools.imp_exp.unpack_tar_gz_archive module
• galaxy.tools.linters package
  • Submodules
  • galaxy.tools.linters.citations module
  • galaxy.tools.linters.command module
  • galaxy.tools.linters.general module
  • galaxy.tools.linters.help module
  • galaxy.tools.linters.inputs module
  • galaxy.tools.linters.outputs module
  • galaxy.tools.linters.stdio module
  • galaxy.tools.linters.tests module
  • galaxy.tools.linters.xml_order module
• galaxy.tools.locations package
  • Submodules
  • galaxy.tools.locations.dockstore module
  • galaxy.tools.locations.file module
  • galaxy.tools.locations.http module
• galaxy.tools.parameters package
  • Submodules
  • galaxy.tools.parameters.basic module
  • galaxy.tools.parameters.dataset_matcher module
  • galaxy.tools.parameters.dynamic_options module
  • galaxy.tools.parameters.grouping module
  • galaxy.tools.parameters.history_query module
  • galaxy.tools.parameters.input_translation module
  • galaxy.tools.parameters.meta module
  • galaxy.tools.parameters.output_collect module
  • galaxy.tools.parameters.sanitize module
  • galaxy.tools.parameters.validation module
  • galaxy.tools.parameters.wrapped module
  • galaxy.tools.parameters.wrapped_json module
• galaxy.tools.parser package
  • Submodules
  • galaxy.tools.parser.cwl module
  • galaxy.tools.parser.error_level module
  • galaxy.tools.parser.factory module
  • galaxy.tools.parser.interface module
  • galaxy.tools.parser.output_actions module
  • galaxy.tools.parser.output_collection_def module
  • galaxy.tools.parser.output_objects module
  • galaxy.tools.parser.util module
  • galaxy.tools.parser.xml module
  • galaxy.tools.parser.yaml module
• galaxy.tools.search package
• galaxy.tools.toolbox package
  • Subpackages
    • galaxy.tools.toolbox.filters package
    • galaxy.tools.toolbox.lineages package
      • Submodules
      • galaxy.tools.toolbox.lineages.factory module
      • galaxy.tools.toolbox.lineages.interface module
  • Submodules
  • galaxy.tools.toolbox.base module
  • galaxy.tools.toolbox.integrated_panel module
  • galaxy.tools.toolbox.panel module
  • galaxy.tools.toolbox.parser module
  • galaxy.tools.toolbox.tags module
  • galaxy.tools.toolbox.watcher module
• galaxy.tools.util package
  • Subpackages
    • galaxy.tools.util.galaxyops package
  • Submodules
  • galaxy.tools.util.maf_utilities module
• galaxy.tools.verify package
  • Subpackages
    • galaxy.tools.verify.asserts package
      • Submodules
      • galaxy.tools.verify.asserts.hdf5 module
      • galaxy.tools.verify.asserts.tabular module
      • galaxy.tools.verify.asserts.text module
      • galaxy.tools.verify.asserts.xml module
  • Submodules
  • galaxy.tools.verify.interactor module
  • galaxy.tools.verify.script module
  • galaxy.tools.verify.test_data module

Submodules

galaxy.tools.cache module

class galaxy.tools.cache.ToolCache

Bases: object

Cache tool definitions to allow quickly reloading the whole toolbox.

__init__()

cleanup()

Remove uninstalled tools from tool cache if they are not on disk anymore or if their content has changed.

Returns list of tool_ids that have been removed.

get_tool(config_filename)

Get the tool at config_filename from the cache if the tool is up to date.

get_removed_tool(config_filename)

get_tool_by_id(tool_id)

Get the tool with the id tool_id from the cache if the tool is up to date.

expire_tool(tool_id)

cache_tool(config_filename, tool)

reset_status()

Reset tracking of new and newly disabled tools.

class galaxy.tools.cache.ToolShedRepositoryCache(app)

Bases: object

Cache installed ToolShedRepository objects.

__init__(app)

add_local_repository(repository)

tool_shed_repositories

rebuild()

get_installed_repository(tool_shed=None, name=None, owner=None, installed_changeset_revision=None, changeset_revision=None, repository_id=None)

galaxy.tools.data_fetch module

galaxy.tools.data_fetch.main(argv=None)

galaxy.tools.data_fetch.elements_tree_map(f, items)

class galaxy.tools.data_fetch.UploadConfig(request, registry)

Bases: object

__init__(request, registry)

get_option(item, key)

Return item[key] if specified otherwise use default from UploadConfig.

This default represents the default for the whole request instead item which is the option for individual files.

ensure_in_working_directory(path, purge_source, in_place)

galaxy.tools.errors module

Functionality for dealing with tool errors.

class galaxy.tools.errors.ErrorReporter(hda, app)

Bases: object

__init__(hda, app)

create_report(user, email='', message='', redact_user_details_in_bugreport=False, **kwd)

send_report(user, email=None, message=None, **kwd)

class galaxy.tools.errors.EmailErrorReporter(hda, app)

Bases: galaxy.tools.errors.ErrorReporter

galaxy.tools.evaluation module

class galaxy.tools.evaluation.ToolEvaluator(app, tool, job, local_working_directory)

Bases: object

An abstraction linking together a tool and a job runtime to evaluate tool inputs in an isolated, testable manner.

__init__(app, tool, job, local_working_directory)

set_compute_environment(compute_environment, get_special=None)

Setup the compute environment and established the outline of the param_dict for evaluating command and config cheetah templates.

build_param_dict(incoming, input_datasets, output_datasets, output_collections, output_paths, job_working_directory, input_paths=[])

Build the dictionary of parameters for substituting into the command line. Each value is wrapped in a InputValueWrapper, which allows all the attributes of the value to be used in the template, but when the __str__ method is called it actually calls the to_param_dict_string method of the associated input.

build()

Build runtime description of job to execute, evaluate command and config templates corresponding to this tool with these inputs on this compute environment.

galaxy.tools.exception_handling module

class galaxy.tools.exception_handling.UCSCOutWrapper(other)

Bases: object

File-like object that throws an exception if it encounters the UCSC limit error lines

__init__(other)

next()

readline()

exception galaxy.tools.exception_handling.UCSCLimitException

Bases: exceptions.Exception

galaxy.tools.execute module

Once state information has been calculated, handle actually executing tools from various states, tracking results, and building implicit dataset collections from matched collections.

galaxy.tools.execute.execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, collection_info=None, workflow_invocation_uuid=None, invocation_step=None, max_num_jobs=None, job_callback=None, completed_jobs=None, workflow_resource_parameters=None)

Execute a tool and return object containing summary (output data, number of failures, etc…).

galaxy.tools.fetcher module

class galaxy.tools.fetcher.ToolLocationFetcher

Bases: object

__init__()

to_tool_path(path_or_uri_like, **kwds)

galaxy.tools.lint module

This modules contains the functions that drive the tool linting framework.

galaxy.tools.lint.lint_tool_source(tool_source, level='all', fail_level='warn', extra_modules=[], skip_types=[], name=None)

galaxy.tools.lint.lint_xml(tool_xml, level='all', fail_level='warn', extra_modules=[], skip_types=[], name=None)

galaxy.tools.lint.lint_tool_source_with(lint_context, tool_source, extra_modules=[])

galaxy.tools.lint.lint_xml_with(lint_context, tool_xml, extra_modules=[])

class galaxy.tools.lint.LintContext(level, skip_types=[], object_name=None)

Bases: object

__init__(level, skip_types=[], object_name=None)

lint(name, lint_func, lint_target)

valid(message, *args)

info(message, *args)

error(message, *args)

warn(message, *args)

failed(fail_level)

galaxy.tools.lint_util module

galaxy.tools.lint_util.is_datasource(tool_xml)

Returns true if the tool is a datasource tool

galaxy.tools.loader module

galaxy.tools.loader.load_tool(path)

galaxy.tools.loader.load_tool_with_refereces(path)

Load XML documentation from file system and preprocesses XML macros.

Return the XML representation of the expanded tree and paths to referenced files that were imported (macros).

galaxy.tools.loader.raw_tool_xml_tree(path)

Load raw (no macro expansion) tree representation of XML represented at the specified path.

galaxy.tools.loader.imported_macro_paths(root)

galaxy.tools.loader.template_macro_params(root)

Look for template macros and populate param_dict (for cheetah) with these.

galaxy.tools.loader_directory module

Utilities for loading and reasoning about unparsed tools in directories.

galaxy.tools.loader_directory.find_possible_tools_from_path(path, recursive=False, enable_beta_formats=False)

Walk a directory and find potential tool files.

galaxy.tools.loader_directory.load_tool_sources_from_path(path, load_exception_handler=<function load_exception_handler>, recursive=False, register_load_errors=False)

Walk a directory and ToolSource objects.

galaxy.tools.loader_directory.load_tool_elements_from_path(path, load_exception_handler=<function load_exception_handler>, recursive=False, register_load_errors=False)

Walk a directory and load tool XML elements.

galaxy.tools.loader_directory.is_tool_load_error(obj)

Predicate to determine if object loaded for tool is a tool error.

galaxy.tools.loader_directory.looks_like_a_tool_xml(path)

Quick check to see if a file looks like it may be a Galaxy XML tool file.

galaxy.tools.loader_directory.is_a_yaml_with_class(path, classes)

Determine if a file is a valid YAML with a supplied class entry.

galaxy.tools.loader_directory.looks_like_a_tool_yaml(path)

Quick check to see if a file looks like it may be a Galaxy YAML tool file.

galaxy.tools.loader_directory.looks_like_a_cwl_artifact(path, classes=None)

Quick check to see if a file looks like it may be a CWL artifact.

galaxy.tools.loader_directory.looks_like_a_tool_cwl(path)

Quick check to see if a file looks like it may be a CWL tool.

galaxy.tools.provided_metadata module

galaxy.tools.provided_metadata.parse_tool_provided_metadata(meta_file, provided_metadata_style=None, job_wrapper=None)

Return a ToolProvidedMetadata object for specified file path.

If meta_file is absent, return a NullToolProvidedMetadata. If provided_metadata_style is None attempt to guess tool provided metadata type.

class galaxy.tools.provided_metadata.BaseToolProvidedMetadata

Bases: object

get_new_datasets(output_name)

Find new datasets for dataset discovery for specified output.

Return a list of such datasets.

Called only in the context of discovering datasets when discover_via=”tool_provided_metadata” is defined in the tool.

has_failed_outputs()

Determine if generation of any of the outputs failed.

get_new_dataset_meta_by_basename(output_name, basename)

For a discovered dataset, get the corresponding metadata entry.

The discovery may have been from explicit listing in this file (returned from get_new_datasets) or via file regex, either way the basename of the file is used to index the fetching of the metadata entry.

get_unnamed_outputs()

Return unnamed outputs dataset introduced for upload 2.0.

Needs more formal specification but see output_collect for how destinations, types, elements, etc… are consumed.

get_dataset_meta(output_name, dataset_id)

Return primary dataset metadata for specified output.

rewrite()

Write metadata back to the file system.

If metadata has not changed via outputs specified as mutable, the implementation class may opt to not re-write the file.

get_new_datasets_for_metadata_collection()

Return all datasets tracked that are not explicit primary outputs.

class galaxy.tools.provided_metadata.NullToolProvidedMetadata

Bases: galaxy.tools.provided_metadata.BaseToolProvidedMetadata

class galaxy.tools.provided_metadata.LegacyToolProvidedMetadata(meta_file, job_wrapper=None)

Bases: galaxy.tools.provided_metadata.BaseToolProvidedMetadata

__init__(meta_file, job_wrapper=None)

get_dataset_meta(output_name, dataset_id)

get_new_dataset_meta_by_basename(output_name, basename)

get_new_datasets(output_name)

has_failed_outputs()

get_unnamed_outputs()

rewrite()

get_new_datasets_for_metadata_collection()

class galaxy.tools.provided_metadata.ToolProvidedMetadata(meta_file)

Bases: galaxy.tools.provided_metadata.BaseToolProvidedMetadata

__init__(meta_file)

get_dataset_meta(output_name, dataset_id)

get_new_dataset_meta_by_basename(output_name, basename)

get_new_datasets(output_name)

has_failed_outputs()

get_unnamed_outputs()

rewrite()

galaxy.tools.repositories module

Provides a subset of app for verifying tools.

class galaxy.tools.repositories.ValidationContext(app_name, security, model, tool_data_path, shed_tool_data_path, tool_data_tables=None, registry=None, hgweb_config_manager=None)

Bases: object

Minimal App object for tool validation.

__init__(app_name, security, model, tool_data_path, shed_tool_data_path, tool_data_tables=None, registry=None, hgweb_config_manager=None)

static from_app(*args, **kwds)

galaxy.tools.special_tools module

galaxy.tools.special_tools.load_lib_tools(toolbox)

galaxy.tools.test module

galaxy.tools.test.parse_tests(tool, tests_source)

Build ToolTestBuilder objects for each “<test>” elements and return default interactor (if any).

galaxy.tools.test.description_from_tool_object(tool, test_index, raw_test_dict)

galaxy.tools.test.require_file(name, value, extra, required_files)

class galaxy.tools.test.ParamContext(name, index=None, parent_context=None)

Bases: object

__init__(name, index=None, parent_context=None)

for_state()

param_names()

extract_value(raw_inputs)

class galaxy.tools.test.RootParamContext

Bases: object

__init__()

for_state()

param_names()

get_index()

galaxy.tools.wrappers module

galaxy.tools.wrappers.DEFAULT_PATH_REWRITER(x)

class galaxy.tools.wrappers.ToolParameterValueWrapper

Bases: object

Base class for object that Wraps a Tool Parameter and Value.

get_display_text(quote=True)

Returns a string containing the value that would be displayed to the user in the tool interface. When quote is True (default), the string is escaped for e.g. command-line usage.

class galaxy.tools.wrappers.RawObjectWrapper(obj)

Bases: galaxy.tools.wrappers.ToolParameterValueWrapper

Wraps an object so that __str__ returns module_name:class_name.

__init__(obj)

class galaxy.tools.wrappers.InputValueWrapper(input, value, other_values={})

Bases: galaxy.tools.wrappers.ToolParameterValueWrapper

Wraps an input so that __str__ gives the “param_dict” representation.

__init__(input, value, other_values={})

class galaxy.tools.wrappers.SelectToolParameterWrapper(input, value, other_values={}, path_rewriter=None)

Bases: galaxy.tools.wrappers.ToolParameterValueWrapper

Wraps a SelectTooParameter so that __str__ returns the selected value, but all other attributes are accessible.

class SelectToolParameterFieldWrapper(input, value, other_values, path_rewriter)

Bases: object

Provide access to any field by name or index for this particular value. Only applicable for dynamic_options selects, which have more than simple ‘options’ defined (name, value, selected).

__init__(input, value, other_values, path_rewriter)

__init__(input, value, other_values={}, path_rewriter=None)

class galaxy.tools.wrappers.DatasetFilenameWrapper(dataset, datatypes_registry=None, tool=None, name=None, dataset_path=None, identifier=None, formats=None)

Bases: galaxy.tools.wrappers.ToolParameterValueWrapper

Wraps a dataset so that __str__ returns the filename, but all other attributes are accessible.

class MetadataWrapper(metadata)

Bases: object

Wraps a Metadata Collection to return MetadataParameters wrapped according to the metadata spec. Methods implemented to match behavior of a Metadata Collection.

__init__(metadata)

get(key, default=None)

items()

__init__(dataset, datatypes_registry=None, tool=None, name=None, dataset_path=None, identifier=None, formats=None)

element_identifier

is_collection

is_of_type(*exts)

class galaxy.tools.wrappers.HasDatasets

Bases: object

paths_as_file(sep='\n')

class galaxy.tools.wrappers.DatasetListWrapper(job_working_directory, datasets, dataset_paths=[], **kwargs)

Bases: list, galaxy.tools.wrappers.ToolParameterValueWrapper, galaxy.tools.wrappers.HasDatasets

__init__(job_working_directory, datasets, dataset_paths=[], **kwargs)

static to_dataset_instances(dataset_instance_sources)

get_datasets_for_group(group)

class galaxy.tools.wrappers.DatasetCollectionWrapper(job_working_directory, has_collection, dataset_paths=[], **kwargs)

Bases: galaxy.tools.wrappers.ToolParameterValueWrapper, galaxy.tools.wrappers.HasDatasets

__init__(job_working_directory, has_collection, dataset_paths=[], **kwargs)

get_datasets_for_group(group)

keys()

is_collection

element_identifier

is_input_supplied

class galaxy.tools.wrappers.ElementIdentifierMapper(input_datasets=None)

Bases: object

Track mapping of dataset collection elements datasets to element identifiers.

__init__(input_datasets=None)

identifier(dataset_value, input_values)