Warning
This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
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:
object
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, 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).
-
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
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¶
-
-
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¶
-
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¶
-
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¶
-
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.
-
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.