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galaxy.tools.cwl package¶
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galaxy.tools.cwl.tool_proxy(tool_path=None, tool_object=None, strict_cwl_validation=True)[source]¶ Provide a proxy object to cwltool data structures to just grab relevant data.
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galaxy.tools.cwl.tool_proxy_from_persistent_representation(persisted_tool, strict_cwl_validation=True)[source]¶
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galaxy.tools.cwl.to_cwl_job(tool, param_dict, local_working_directory)[source]¶ tool is Galaxy’s representation of the tool and param_dict is the parameter dictionary with wrapped values.
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galaxy.tools.cwl.to_galaxy_parameters(tool, as_dict)[source]¶ Tool is Galaxy’s representation of the tool and as_dict is a Galaxified representation of the input json (no paths, HDA references for instance).
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galaxy.tools.cwl.needs_shell_quoting()¶ search(string[, pos[, endpos]]) –> match object or None. Scan through string looking for a match, and return a corresponding match object instance. Return None if no position in the string matches.
Submodules¶
galaxy.tools.cwl.cwltool_deps module¶
Logic for dealing with cwltool as an optional dependency.
Use this as the import interface for cwltool and just call
ensure_cwltool_available() before using any of the imported
functionality at runtime.
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galaxy.tools.cwl.cwltool_deps.needs_shell_quoting()¶ search(string[, pos[, endpos]]) –> match object or None. Scan through string looking for a match, and return a corresponding match object instance. Return None if no position in the string matches.
galaxy.tools.cwl.parser module¶
This module provides proxy objects around objects from the common workflow language reference implementation library cwltool. These proxies adapt cwltool to Galaxy features and abstract the library away from the rest of the framework.
galaxy.tools.cwl.representation module¶
This module is responsible for converting between Galaxy’s tool input description and the CWL description for a job json.
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class
galaxy.tools.cwl.representation.TypeRepresentation(name, galaxy_param_type, label, collection_type)¶ Bases:
tuple-
collection_type¶ Alias for field number 3
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galaxy_param_type¶ Alias for field number 1
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label¶ Alias for field number 2
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name¶ Alias for field number 0
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uses_param()¶
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galaxy.tools.cwl.representation.dataset_wrapper_to_directory_json(inputs_dir, dataset_wrapper)[source]¶
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galaxy.tools.cwl.representation.to_cwl_job(tool, param_dict, local_working_directory)[source]¶ tool is Galaxy’s representation of the tool and param_dict is the parameter dictionary with wrapped values.
galaxy.tools.cwl.runtime_actions module¶
galaxy.tools.cwl.schema module¶
Abstraction around cwltool and related libraries for loading a CWL artifact.
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class
galaxy.tools.cwl.schema.RawProcessReference(process_object, uri)¶ Bases:
tuple-
process_object¶ Alias for field number 0
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uri¶ Alias for field number 1
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class
galaxy.tools.cwl.schema.ProcessDefinition(process_object, metadata, document_loader, avsc_names, raw_process_reference)¶ Bases:
tuple-
avsc_names¶ Alias for field number 3
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document_loader¶ Alias for field number 2
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metadata¶ Alias for field number 1
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process_object¶ Alias for field number 0
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raw_process_reference¶ Alias for field number 4
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galaxy.tools.cwl.util module¶
Client-centric CWL-related utilities.
Used to share code between the Galaxy test framework and other Galaxy CWL clients (e.g. Planemo).
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galaxy.tools.cwl.util.output_properties(path=None, content=None, basename=None, pseduo_location=False)[source]¶
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galaxy.tools.cwl.util.galactic_job_json(job, test_data_directory, upload_func, collection_create_func, tool_or_workflow='workflow')[source]¶ Adapt a CWL job object to the Galaxy API.
CWL derived tools in Galaxy can consume a job description sort of like CWL job objects via the API but paths need to be replaced with datasets and records and arrays with collection references. This function will stage files and modify the job description to adapt to these changes for Galaxy.