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galaxy.tools.actions package

class galaxy.tools.actions.ToolExecutionCache(trans)

Bases: object

An object mean to cache calculation caused by repeatedly evaluting the same tool by the same user with slightly different parameters.

__init__(trans)

get_chrom_info(tool_id, input_dbkey)

class galaxy.tools.actions.ToolAction

Bases: object

The actions to be taken when a tool is run (after parameters have been converted and validated).

execute(tool, trans, incoming=None, set_output_hid=True)

class galaxy.tools.actions.DefaultToolAction

Bases: object

Default tool action is to run an external command

produces_real_jobs = True

collect_input_dataset_collections(tool, param_values)

execute(tool, trans, incoming=None, return_job=False, set_output_hid=True, history=None, job_params=None, rerun_remap_job_id=None, execution_cache=None, dataset_collection_elements=None, completed_job=None, collection_info=None)

Executes a tool, creating job and tool outputs, associating them, and submitting the job to the job queue. If history is not specified, use trans.history as destination for tool’s output datasets.

get_output_name(output, dataset, tool, on_text, trans, incoming, history, params, job_params)

set_metadata_defaults(output, dataset, tool, on_text, trans, incoming, history, params, job_params)

This allows to map names of input files to metadata default values. Example:

<data format=”tabular” name=”output” label=”Tabular output, aggregates data from individual_inputs” >

<actions>

<action name=”column_names” type=”metadata” default=”${‘,’.join([input.name for input in $individual_inputs ])}” />

</actions>

</data>

class galaxy.tools.actions.OutputCollections(trans, history, tool, tool_action, input_collections, dataset_collection_elements, on_text, incoming, params, job_params, tags)

Bases: object

Keeps track of collections (DC or HDCA) created by actions.

Actions do fairly different things depending on whether we are creating just part of an collection or a whole output collection (mapping_over_collection parameter).

__init__(trans, history, tool, tool_action, input_collections, dataset_collection_elements, on_text, incoming, params, job_params, tags)

create_collection(output, name, collection_type=None, **element_kwds)

galaxy.tools.actions.on_text_for_names(input_names)

galaxy.tools.actions.filter_output(output, incoming)

galaxy.tools.actions.get_ext_or_implicit_ext(hda)

galaxy.tools.actions.determine_output_format(output, parameter_context, input_datasets, input_dataset_collections, random_input_ext, python_template_version='3')

Determines the output format for a dataset based on an abstract description of the output (galaxy.tool_util.parser.ToolOutput), the parameter wrappers, a map of the input datasets (name => HDA), and the last input extensions in the tool form.

TODO: Don’t deal with XML here - move this logic into ToolOutput. TODO: Make the input extension used deterministic instead of random.

Submodules

galaxy.tools.actions.data_manager module

class galaxy.tools.actions.data_manager.DataManagerToolAction

Bases: galaxy.tools.actions.DefaultToolAction

Tool action used for Data Manager Tools

execute(tool, trans, **kwds)

galaxy.tools.actions.data_source module

class galaxy.tools.actions.data_source.DataSourceToolAction

Bases: galaxy.tools.actions.DefaultToolAction

Tool action used for Data Source Tools

galaxy.tools.actions.history_imp_exp module

class galaxy.tools.actions.history_imp_exp.ImportHistoryToolAction

Bases: galaxy.tools.actions.ToolAction

Tool action used for importing a history to an archive.

produces_real_jobs = True

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

class galaxy.tools.actions.history_imp_exp.ExportHistoryToolAction

Bases: galaxy.tools.actions.ToolAction

Tool action used for exporting a history to an archive.

produces_real_jobs = True

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

galaxy.tools.actions.metadata module

class galaxy.tools.actions.metadata.SetMetadataToolAction

Bases: galaxy.tools.actions.ToolAction

Tool action used for setting external metadata on an existing dataset

produces_real_jobs = False

execute(tool, trans, incoming={}, set_output_hid=False, overwrite=True, history=None, job_params=None, **kwargs)

Execute using a web transaction.

execute_via_app(tool, app, session_id, history_id, user=None, incoming={}, set_output_hid=False, overwrite=True, history=None, job_params=None)

Execute using application.

galaxy.tools.actions.model_operations module

class galaxy.tools.actions.model_operations.ModelOperationToolAction

Bases: galaxy.tools.actions.DefaultToolAction

produces_real_jobs = False

check_inputs_ready(tool, trans, incoming, history, execution_cache=None, collection_info=None)

execute(tool, trans, incoming={}, set_output_hid=False, overwrite=True, history=None, job_params=None, execution_cache=None, collection_info=None, **kwargs)

galaxy.tools.actions.upload module

class galaxy.tools.actions.upload.BaseUploadToolAction

Bases: galaxy.tools.actions.ToolAction

produces_real_jobs = True

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

class galaxy.tools.actions.upload.UploadToolAction

Bases: galaxy.tools.actions.upload.BaseUploadToolAction

class galaxy.tools.actions.upload.FetchUploadToolAction

Bases: galaxy.tools.actions.upload.BaseUploadToolAction

galaxy.tools.actions.upload_common module

galaxy.tools.actions.upload_common.validate_datatype_extension(datatypes_registry, ext)

galaxy.tools.actions.upload_common.validate_url(url, ip_whitelist)

galaxy.tools.actions.upload_common.persist_uploads(params, trans)

Turn any uploads in the submitted form to persisted files.

galaxy.tools.actions.upload_common.handle_library_params(trans, params, folder_id, replace_dataset=None)

galaxy.tools.actions.upload_common.new_upload(trans, cntrller, uploaded_dataset, library_bunch=None, history=None, state=None, tag_list=None)

galaxy.tools.actions.upload_common.get_uploaded_datasets(trans, cntrller, params, dataset_upload_inputs, library_bunch=None, history=None)

galaxy.tools.actions.upload_common.create_paramfile(trans, uploaded_datasets)

Create the upload tool’s JSON “param” file.

galaxy.tools.actions.upload_common.create_job(trans, params, tool, json_file_path, outputs, folder=None, history=None, job_params=None)

Create the upload job.

galaxy.tools.actions.upload_common.active_folders(trans, folder)