galaxy.tools.actions package
- class galaxy.tools.actions.ToolExecutionCache(trans)[source]
Bases:
object
An object mean to cache calculation caused by repeatedly evaluting the same tool by the same user with slightly different parameters.
- class galaxy.tools.actions.ToolAction[source]
Bases:
object
The actions to be taken when a tool is run (after parameters have been converted and validated).
- class galaxy.tools.actions.DefaultToolAction[source]
Bases:
ToolAction
Default tool action is to run an external command
- produces_real_jobs = True
- 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, job_callback=None, preferred_object_store_id=None, flush_job=True, skip=False)[source]
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.
- class galaxy.tools.actions.OutputCollections(trans, history, tool, tool_action, input_collections, dataset_collection_elements, on_text, incoming, params, job_params, tags, hdca_tags)[source]
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).
- galaxy.tools.actions.determine_output_format(output: ToolOutput, parameter_context, input_datasets, input_dataset_collections, random_input_ext, python_template_version='3', execution_cache=None)[source]
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: Make the input extension used deterministic instead of random.
Submodules
galaxy.tools.actions.data_manager module
- class galaxy.tools.actions.data_manager.DataManagerToolAction[source]
Bases:
DefaultToolAction
Tool action used for Data Manager Tools
galaxy.tools.actions.data_source module
- class galaxy.tools.actions.data_source.DataSourceToolAction[source]
Bases:
DefaultToolAction
Tool action used for Data Source Tools
galaxy.tools.actions.history_imp_exp module
- class galaxy.tools.actions.history_imp_exp.ImportHistoryToolAction[source]
Bases:
ToolAction
Tool action used for importing a history to an archive.
- produces_real_jobs = True
galaxy.tools.actions.metadata module
- class galaxy.tools.actions.metadata.SetMetadataToolAction[source]
Bases:
ToolAction
Tool action used for setting external metadata on an existing dataset
- produces_real_jobs = False
galaxy.tools.actions.model_operations module
- class galaxy.tools.actions.model_operations.ModelOperationToolAction[source]
Bases:
DefaultToolAction
- produces_real_jobs = False
- check_inputs_ready(tool, trans, incoming, history, execution_cache=None, collection_info=None)[source]
- execute(tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, job_params=None, execution_cache=None, collection_info=None, job_callback=None, skip=False, **kwargs)[source]
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.
galaxy.tools.actions.upload module
- class galaxy.tools.actions.upload.BaseUploadToolAction[source]
Bases:
ToolAction
- produces_real_jobs = True
- class galaxy.tools.actions.upload.UploadToolAction[source]
Bases:
BaseUploadToolAction
- class galaxy.tools.actions.upload.FetchUploadToolAction[source]
Bases:
BaseUploadToolAction
galaxy.tools.actions.upload_common module
- galaxy.tools.actions.upload_common.persist_uploads(params, trans)[source]
Turn any uploads in the submitted form to persisted files.
- class galaxy.tools.actions.upload_common.LibraryParams(roles: List[galaxy.model.Role], tags: List[str] | NoneType, template: galaxy.model.FormDefinition | NoneType, template_field_contents: Dict[str, str], folder: galaxy.model.LibraryFolder, message: str, replace_dataset: galaxy.model.LibraryDataset | NoneType)[source]
Bases:
object
- template: FormDefinition | None
- folder: LibraryFolder
- replace_dataset: LibraryDataset | None
- galaxy.tools.actions.upload_common.handle_library_params(trans, params, folder_id: int, replace_dataset: LibraryDataset | None = None) LibraryParams [source]
- galaxy.tools.actions.upload_common.new_upload(trans: ProvidesUserContext, cntrller, uploaded_dataset, library_bunch=None, history=None, state=None, tag_list=None)[source]
- galaxy.tools.actions.upload_common.get_uploaded_datasets(trans, cntrller, params, dataset_upload_inputs, library_bunch=None, history=None)[source]
- galaxy.tools.actions.upload_common.create_paramfile(trans, uploaded_datasets)[source]
Create the upload tool’s JSON “param” file.