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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.

__init__(trans)[source]

Initialize self. See help(type(self)) for accurate signature.

get_chrom_info(tool_id, input_dbkey)[source]
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).

execute(tool, trans, incoming=None, set_output_hid=True)[source]
class galaxy.tools.actions.DefaultToolAction[source]

Bases: object

Default tool action is to run an external command

produces_real_jobs = True
collect_input_dataset_collections(tool, param_values)[source]
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, flush_job=True)[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.

get_output_name(output, dataset=None, tool=None, on_text=None, trans=None, incoming=None, history=None, params=None, job_params=None)[source]
set_metadata_defaults(output, dataset, tool, on_text, trans, incoming, history, params, job_params)[source]

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, 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).

__init__(trans, history, tool, tool_action, input_collections, dataset_collection_elements, on_text, incoming, params, job_params, tags, hdca_tags)[source]

Initialize self. See help(type(self)) for accurate signature.

create_collection(output, name, collection_type=None, completed_job=None, propagate_hda_tags=True, **element_kwds)[source]
galaxy.tools.actions.on_text_for_names(input_names)[source]
galaxy.tools.actions.filter_output(tool, output, incoming)[source]
galaxy.tools.actions.get_ext_or_implicit_ext(hda)[source]
galaxy.tools.actions.determine_output_format(output, 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: 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[source]

Bases: galaxy.tools.actions.DefaultToolAction

Tool action used for Data Manager Tools

execute(tool, trans, **kwds)[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.data_source module

class galaxy.tools.actions.data_source.DataSourceToolAction[source]

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[source]

Bases: galaxy.tools.actions.ToolAction

Tool action used for importing a history to an archive.

produces_real_jobs = True
execute(tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, **kwargs)[source]
class galaxy.tools.actions.history_imp_exp.ExportHistoryToolAction[source]

Bases: galaxy.tools.actions.ToolAction

Tool action used for exporting a history to an archive.

produces_real_jobs = True
execute(tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, **kwargs)[source]

galaxy.tools.actions.metadata module

class galaxy.tools.actions.metadata.SetMetadataToolAction[source]

Bases: galaxy.tools.actions.ToolAction

Tool action used for setting external metadata on an existing dataset

produces_real_jobs = False
execute(tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, job_params=None, **kwargs)[source]

Execute using a web transaction.

execute_via_app(tool, app, session_id, history_id, user=None, incoming=None, set_output_hid=False, overwrite=True, history=None, job_params=None)[source]

Execute using application.

galaxy.tools.actions.model_operations module

class galaxy.tools.actions.model_operations.ModelOperationToolAction[source]

Bases: galaxy.tools.actions.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, **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: galaxy.tools.actions.ToolAction

produces_real_jobs = True
execute(tool, trans, incoming=None, history=None, **kwargs)[source]
class galaxy.tools.actions.upload.UploadToolAction[source]

Bases: galaxy.tools.actions.upload.BaseUploadToolAction

class galaxy.tools.actions.upload.FetchUploadToolAction[source]

Bases: galaxy.tools.actions.upload.BaseUploadToolAction

galaxy.tools.actions.upload_common module

galaxy.tools.actions.upload_common.validate_datatype_extension(datatypes_registry, ext)[source]
galaxy.tools.actions.upload_common.validate_url(url, ip_allowlist)[source]
galaxy.tools.actions.upload_common.persist_uploads(params, trans)[source]

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)[source]
galaxy.tools.actions.upload_common.new_upload(trans, 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.

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

Create the upload job.

galaxy.tools.actions.upload_common.active_folders(trans, folder)[source]