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galaxy.tools.cwl package¶

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.

galaxy.tools.cwl.tool_proxy_from_persistent_representation(persisted_tool, strict_cwl_validation=True)[source]¶

galaxy.tools.cwl.workflow_proxy(workflow_path, strict_cwl_validation=True)[source]¶

galaxy.tools.cwl.handle_outputs(job_directory=None)[source]¶

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.

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).

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.

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.cwltool_deps.ensure_cwltool_available()[source]¶

Assert optional dependencies proxied via this module are available at runtime.

Throw an ImportError with a description of the problem if they do not exist.

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.parser.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.

galaxy.tools.cwl.parser.load_job_proxy(job_directory, strict_cwl_validation=True)[source]¶

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.

class galaxy.tools.cwl.representation.TypeRepresentation(name, galaxy_param_type, label, collection_type)¶

Bases: tuple

collection_type¶: Alias for field number 3

galaxy_param_type¶: Alias for field number 1

label¶: Alias for field number 2

name¶: Alias for field number 0

uses_param()¶

galaxy.tools.cwl.representation.type_representation_from_name(type_representation_name)[source]¶

galaxy.tools.cwl.representation.type_descriptions_for_field_types(field_types)[source]¶

galaxy.tools.cwl.representation.dataset_wrapper_to_file_json(inputs_dir, dataset_wrapper)[source]¶

galaxy.tools.cwl.representation.dataset_wrapper_to_directory_json(inputs_dir, dataset_wrapper)[source]¶

galaxy.tools.cwl.representation.collection_wrapper_to_array(inputs_dir, wrapped_value)[source]¶

galaxy.tools.cwl.representation.collection_wrapper_to_record(inputs_dir, wrapped_value)[source]¶

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.representation.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).

galaxy.tools.cwl.representation.field_to_field_type(field)[source]¶

galaxy.tools.cwl.runtime_actions module¶

galaxy.tools.cwl.runtime_actions.handle_outputs(job_directory=None)[source]¶

galaxy.tools.cwl.schema module¶

Abstraction around cwltool and related libraries for loading a CWL artifact.

class galaxy.tools.cwl.schema.RawProcessReference(process_object, uri)¶

Bases: tuple

process_object¶: Alias for field number 0

uri¶: Alias for field number 1

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

document_loader¶: Alias for field number 2

metadata¶: Alias for field number 1

process_object¶: Alias for field number 0

raw_process_reference¶: Alias for field number 4

class galaxy.tools.cwl.schema.SchemaLoader(strict=True)[source]¶

Bases: object

__init__(strict=True)[source]¶

raw_document_loader¶

raw_process_reference(path)[source]¶

raw_process_reference_for_object(object, uri=None)[source]¶

process_definition(raw_reference)[source]¶

tool(**kwds)[source]¶