cwl_utils.parser.cwl_v1_0

Attributes

`strtype`
`inttype`
`floattype`
`booltype`
`None_type`
`Any_type`
`DocumentedProxyLoader`
`PrimitiveTypeLoader`	Names of salad data types (based on Avro schema declarations).
`AnyLoader`	The Any type validates for any non-null value.
`RecordFieldLoader`
`RecordSchemaLoader`
`EnumSchemaLoader`
`ArraySchemaLoader`
`MapSchemaLoader`
`UnionSchemaLoader`
`CWLTypeLoader`	Extends primitive types with the concept of a file and directory as a builtin type.
`CWLArraySchemaLoader`
`CWLRecordFieldLoader`
`CWLRecordSchemaLoader`
`FileLoader`
`DirectoryLoader`
`CWLObjectTypeLoader`
`union_of_None_type_or_CWLObjectTypeLoader`
`array_of_union_of_None_type_or_CWLObjectTypeLoader`
`map_of_union_of_None_type_or_CWLObjectTypeLoader`
`CWLInputFileLoader`
`CWLVersionLoader`	Current version symbol for CWL documents.
`SchemaBaseProxyLoader`
`ParameterProxyLoader`
`ExpressionLoader`
`InputBindingProxyLoader`
`OutputBindingProxyLoader`
`InputSchemaProxyLoader`
`OutputSchemaProxyLoader`
`InputRecordFieldLoader`
`InputRecordSchemaLoader`
`InputEnumSchemaLoader`
`InputArraySchemaLoader`
`InputParameterTypeLoader`
`union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype`
`array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype`
`OutputRecordFieldLoader`
`OutputRecordSchemaLoader`
`OutputEnumSchemaLoader`
`OutputArraySchemaLoader`
`OutputParameterTypeLoader`
`union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype`
`array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype`
`InputParameterLoader`
`OutputParameterLoader`
`ProcessRequirementProxyLoader`
`ProcessProxyLoader`
`InlineJavascriptRequirementLoader`
`SchemaDefRequirementLoader`
`EnvironmentDefLoader`
`CommandLineBindingLoader`
`CommandOutputBindingLoader`
`CommandInputRecordFieldLoader`
`CommandInputRecordSchemaLoader`
`CommandInputEnumSchemaLoader`
`CommandInputArraySchemaLoader`
`CommandOutputRecordFieldLoader`
`CommandOutputRecordSchemaLoader`
`CommandOutputEnumSchemaLoader`
`CommandOutputArraySchemaLoader`
`CommandInputParameterTypeLoader`
`union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype`
`array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype`
`CommandInputParameterLoader`
`stdoutLoader`	Only valid as a `type` for a `CommandLineTool` output with no `outputBinding` set.
`stderrLoader`	Only valid as a `type` for a `CommandLineTool` output with no `outputBinding` set.
`CommandOutputParameterTypeLoader`
`union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype`
`array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype`
`CommandOutputParameterLoader`
`CommandLineToolLoader`
`DockerRequirementLoader`
`SoftwareRequirementLoader`
`SoftwarePackageLoader`
`DirentLoader`
`InitialWorkDirRequirementLoader`
`EnvVarRequirementLoader`
`ShellCommandRequirementLoader`
`ResourceRequirementLoader`
`ExpressionToolOutputParameterLoader`
`ExpressionToolLoader`
`LinkMergeMethodLoader`	The input link merge method, described in WorkflowStepInput.
`WorkflowOutputParameterLoader`
`SinkProxyLoader`
`WorkflowStepInputLoader`
`WorkflowStepOutputLoader`
`ScatterMethodLoader`	The scatter method, as described in workflow step scatter.
`WorkflowStepLoader`
`WorkflowLoader`
`SubworkflowFeatureRequirementLoader`
`ScatterFeatureRequirementLoader`
`MultipleInputFeatureRequirementLoader`
`StepInputExpressionRequirementLoader`
`LoadListingRequirementLoader`
`InplaceUpdateRequirementLoader`
`SecretsLoader`
`TimeLimitLoader`
`WorkReuseLoader`
`NetworkAccessLoader`
`ProcessGeneratorLoader`
`MPIRequirementLoader`
`CUDARequirementLoader`
`ShmSizeLoader`
`array_of_strtype`
`union_of_None_type_or_strtype_or_array_of_strtype`
`uri_strtype_True_False_None_None`
`union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype`
`array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype`
`union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype`
`typedsl_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype_2`
`array_of_RecordFieldLoader`
`union_of_None_type_or_array_of_RecordFieldLoader`
`idmap_fields_union_of_None_type_or_array_of_RecordFieldLoader`
`Record_nameLoader`
`typedsl_Record_nameLoader_2`
`union_of_None_type_or_strtype`
`uri_union_of_None_type_or_strtype_True_False_None_None`
`uri_array_of_strtype_True_False_None_None`
`Enum_nameLoader`
`typedsl_Enum_nameLoader_2`
`uri_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype_False_True_2_None`
`Array_nameLoader`
`typedsl_Array_nameLoader_2`
`Map_nameLoader`
`typedsl_Map_nameLoader_2`
`Union_nameLoader`
`typedsl_Union_nameLoader_2`
`union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype`
`array_of_union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype`
`union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype`
`uri_union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype_False_True_2_None`
`typedsl_union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype_2`
`array_of_CWLRecordFieldLoader`
`union_of_None_type_or_array_of_CWLRecordFieldLoader`
`idmap_fields_union_of_None_type_or_array_of_CWLRecordFieldLoader`
`File_classLoader`
`uri_File_classLoader_False_True_None_None`
`uri_union_of_None_type_or_strtype_False_False_None_None`
`union_of_None_type_or_inttype`
`union_of_FileLoader_or_DirectoryLoader`
`array_of_union_of_FileLoader_or_DirectoryLoader`
`union_of_None_type_or_array_of_union_of_FileLoader_or_DirectoryLoader`
`uri_union_of_None_type_or_strtype_True_False_None_True`
`Directory_classLoader`
`uri_Directory_classLoader_False_True_None_None`
`union_of_strtype_or_ExpressionLoader`
`array_of_union_of_strtype_or_ExpressionLoader`
`union_of_None_type_or_strtype_or_ExpressionLoader_or_array_of_union_of_strtype_or_ExpressionLoader`
`union_of_None_type_or_booltype`
`union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype`
`typedsl_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_2`
`union_of_None_type_or_InputBindingProxyLoader`
`array_of_InputRecordFieldLoader`
`union_of_None_type_or_array_of_InputRecordFieldLoader`
`idmap_fields_union_of_None_type_or_array_of_InputRecordFieldLoader`
`uri_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_False_True_2_None`
`union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype`
`typedsl_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_2`
`union_of_None_type_or_OutputBindingProxyLoader`
`array_of_OutputRecordFieldLoader`
`union_of_None_type_or_array_of_OutputRecordFieldLoader`
`idmap_fields_union_of_None_type_or_array_of_OutputRecordFieldLoader`
`uri_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_False_True_2_None`
`union_of_None_type_or_strtype_or_array_of_strtype_or_ExpressionLoader`
`uri_union_of_None_type_or_strtype_or_array_of_strtype_or_ExpressionLoader_True_False_None_True`
`union_of_None_type_or_InputParameterTypeLoader`
`typedsl_union_of_None_type_or_InputParameterTypeLoader_2`
`union_of_None_type_or_strtype_or_ExpressionLoader`
`uri_union_of_None_type_or_strtype_or_ExpressionLoader_True_False_None_True`
`array_of_InputParameterLoader`
`idmap_inputs_array_of_InputParameterLoader`
`array_of_OutputParameterLoader`
`idmap_outputs_array_of_OutputParameterLoader`
union_of_LoadListingRequirementLoader_or_EnvVarRequirementLoader_or_WorkReuseLoader_or_DockerRequirementLoader_or_SoftwareRequirementLoader_or_InitialWorkDirRequirementLoader_or_ScatterFeatureRequirementLoader_or_MPIRequirementLoader_or_SchemaDefRequirementLoader_or_InlineJavascriptRequirementLoader_or_InplaceUpdateRequirementLoader_or_CUDARequirementLoader_or_ResourceRequirementLoader_or_StepInputExpressionRequirementLoader_or_MultipleInputFeatureRequirementLoader_or_SubworkflowFeatureRequirementLoader_or_ShellCommandRequirementLoader_or_TimeLimitLoader_or_SecretsLoader_or_ShmSizeLoader_or_NetworkAccessLoader
`array_of_ProcessRequirementProxyLoader`
`union_of_None_type_or_array_of_ProcessRequirementProxyLoader`
`idmap_requirements_union_of_None_type_or_array_of_ProcessRequirementProxyLoader`
`union_of_ProcessRequirementProxyLoader_or_Any_type`
`array_of_union_of_ProcessRequirementProxyLoader_or_Any_type`
`union_of_None_type_or_array_of_union_of_ProcessRequirementProxyLoader_or_Any_type`
`idmap_hints_union_of_None_type_or_array_of_union_of_ProcessRequirementProxyLoader_or_Any_type`
`union_of_None_type_or_CWLVersionLoader`
`uri_union_of_None_type_or_CWLVersionLoader_False_True_None_None`
`InlineJavascriptRequirement_classLoader`
`uri_InlineJavascriptRequirement_classLoader_False_True_None_None`
`union_of_None_type_or_array_of_strtype`
`SchemaDefRequirement_classLoader`
`uri_SchemaDefRequirement_classLoader_False_True_None_None`
`union_of_InputRecordSchemaLoader_or_InputArraySchemaLoader_or_InputEnumSchemaLoader`
`array_of_InputSchemaProxyLoader`
`union_of_None_type_or_strtype_or_ExpressionLoader_or_array_of_strtype`
`union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype`
`typedsl_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_2`
`union_of_None_type_or_CommandLineBindingLoader`
`array_of_CommandInputRecordFieldLoader`
`union_of_None_type_or_array_of_CommandInputRecordFieldLoader`
`idmap_fields_union_of_None_type_or_array_of_CommandInputRecordFieldLoader`
`uri_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_False_True_2_None`
`union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype`
`typedsl_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_2`
`union_of_None_type_or_CommandOutputBindingLoader`
`array_of_CommandOutputRecordFieldLoader`
`union_of_None_type_or_array_of_CommandOutputRecordFieldLoader`
`idmap_fields_union_of_None_type_or_array_of_CommandOutputRecordFieldLoader`
`uri_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_False_True_2_None`
`union_of_None_type_or_CommandInputParameterTypeLoader`
`typedsl_union_of_None_type_or_CommandInputParameterTypeLoader_2`
`union_of_None_type_or_CommandOutputParameterTypeLoader`
`typedsl_union_of_None_type_or_CommandOutputParameterTypeLoader_2`
`CommandLineTool_classLoader`
`uri_CommandLineTool_classLoader_False_True_None_None`
`array_of_CommandInputParameterLoader`
`idmap_inputs_array_of_CommandInputParameterLoader`
`array_of_CommandOutputParameterLoader`
`idmap_outputs_array_of_CommandOutputParameterLoader`
`union_of_strtype_or_ExpressionLoader_or_CommandLineBindingLoader`
`array_of_union_of_strtype_or_ExpressionLoader_or_CommandLineBindingLoader`
`union_of_None_type_or_array_of_union_of_strtype_or_ExpressionLoader_or_CommandLineBindingLoader`
`array_of_inttype`
`union_of_None_type_or_array_of_inttype`
`DockerRequirement_classLoader`
`uri_DockerRequirement_classLoader_False_True_None_None`
`SoftwareRequirement_classLoader`
`uri_SoftwareRequirement_classLoader_False_True_None_None`
`array_of_SoftwarePackageLoader`
`idmap_packages_array_of_SoftwarePackageLoader`
`uri_union_of_None_type_or_array_of_strtype_False_False_None_True`
`InitialWorkDirRequirement_classLoader`
`uri_InitialWorkDirRequirement_classLoader_False_True_None_None`
`union_of_FileLoader_or_DirectoryLoader_or_DirentLoader_or_strtype_or_ExpressionLoader`
`array_of_union_of_FileLoader_or_DirectoryLoader_or_DirentLoader_or_strtype_or_ExpressionLoader`
`union_of_array_of_union_of_FileLoader_or_DirectoryLoader_or_DirentLoader_or_strtype_or_ExpressionLoader_or_strtype_or_ExpressionLoader`
`EnvVarRequirement_classLoader`
`uri_EnvVarRequirement_classLoader_False_True_None_None`
`array_of_EnvironmentDefLoader`
`idmap_envDef_array_of_EnvironmentDefLoader`
`ShellCommandRequirement_classLoader`
`uri_ShellCommandRequirement_classLoader_False_True_None_None`
`ResourceRequirement_classLoader`
`uri_ResourceRequirement_classLoader_False_True_None_None`
`union_of_None_type_or_inttype_or_strtype_or_ExpressionLoader`
`union_of_None_type_or_OutputParameterTypeLoader`
`typedsl_union_of_None_type_or_OutputParameterTypeLoader_2`
`ExpressionTool_classLoader`
`uri_ExpressionTool_classLoader_False_True_None_None`
`array_of_ExpressionToolOutputParameterLoader`
`idmap_outputs_array_of_ExpressionToolOutputParameterLoader`
`uri_union_of_None_type_or_strtype_or_array_of_strtype_False_False_1_None`
`union_of_None_type_or_LinkMergeMethodLoader`
`uri_union_of_None_type_or_strtype_or_array_of_strtype_False_False_2_None`
`array_of_WorkflowStepInputLoader`
`idmap_in__array_of_WorkflowStepInputLoader`
`union_of_strtype_or_WorkflowStepOutputLoader`
`array_of_union_of_strtype_or_WorkflowStepOutputLoader`
`union_of_array_of_union_of_strtype_or_WorkflowStepOutputLoader`
`uri_union_of_array_of_union_of_strtype_or_WorkflowStepOutputLoader_True_False_None_None`
`array_of_Any_type`
`union_of_None_type_or_array_of_Any_type`
`idmap_hints_union_of_None_type_or_array_of_Any_type`
`union_of_ExpressionToolLoader_or_WorkflowLoader_or_ProcessGeneratorLoader_or_CommandLineToolLoader`
`union_of_strtype_or_ProcessProxyLoader`
`uri_union_of_strtype_or_ProcessProxyLoader_False_False_None_None`
`uri_union_of_None_type_or_strtype_or_array_of_strtype_False_False_0_None`
`union_of_None_type_or_ScatterMethodLoader`
`uri_union_of_None_type_or_ScatterMethodLoader_False_True_None_None`
`Workflow_classLoader`
`uri_Workflow_classLoader_False_True_None_None`
`array_of_WorkflowOutputParameterLoader`
`idmap_outputs_array_of_WorkflowOutputParameterLoader`
`array_of_WorkflowStepLoader`
`union_of_array_of_WorkflowStepLoader`
`idmap_steps_union_of_array_of_WorkflowStepLoader`
`SubworkflowFeatureRequirement_classLoader`
`uri_SubworkflowFeatureRequirement_classLoader_False_True_None_None`
`ScatterFeatureRequirement_classLoader`
`uri_ScatterFeatureRequirement_classLoader_False_True_None_None`
`MultipleInputFeatureRequirement_classLoader`
`uri_MultipleInputFeatureRequirement_classLoader_False_True_None_None`
`StepInputExpressionRequirement_classLoader`
`uri_StepInputExpressionRequirement_classLoader_False_True_None_None`
`uri_strtype_False_True_None_None`
`LoadListingEnumLoader`
`union_of_LoadListingEnumLoader`
`uri_array_of_strtype_False_False_0_None`
`union_of_inttype_or_strtype`
`union_of_booltype_or_strtype`
`union_of_inttype_or_ExpressionLoader`
`union_of_strtype_or_array_of_strtype`
`union_of_None_type_or_inttype_or_ExpressionLoader`
`union_of_CommandLineToolLoader_or_ExpressionToolLoader_or_WorkflowLoader_or_ProcessGeneratorLoader`
`array_of_union_of_CommandLineToolLoader_or_ExpressionToolLoader_or_WorkflowLoader_or_ProcessGeneratorLoader`
`union_of_CommandLineToolLoader_or_ExpressionToolLoader_or_WorkflowLoader_or_ProcessGeneratorLoader_or_array_of_union_of_CommandLineToolLoader_or_ExpressionToolLoader_or_WorkflowLoader_or_ProcessGeneratorLoader`

Classes

`CWLArraySchema`	Mark classes than have a save() and fromDoc() function.
`CWLRecordField`	A field of a record.
`CWLRecordSchema`	Mark classes than have a save() and fromDoc() function.
`File`	Represents a file (or group of files when `secondaryFiles` is provided) that will be accessible by tools using standard POSIX file system call API such as open(2) and read(2).
`Directory`	Represents a directory to present to a command line tool.
`SchemaBase`	Mark classes than have a save() and fromDoc() function.
`Parameter`	Define an input or output parameter to a process.
`InputBinding`	Mark classes than have a save() and fromDoc() function.
`OutputBinding`	Mark classes than have a save() and fromDoc() function.
`InputSchema`	Mark classes than have a save() and fromDoc() function.
`OutputSchema`	Mark classes than have a save() and fromDoc() function.
`InputRecordField`	A field of a record.
`InputRecordSchema`	Mark classes than have a save() and fromDoc() function.
`InputEnumSchema`	Define an enumerated type.
`InputArraySchema`	Mark classes than have a save() and fromDoc() function.
`OutputRecordField`	A field of a record.
`OutputRecordSchema`	Mark classes than have a save() and fromDoc() function.
`OutputEnumSchema`	Define an enumerated type.
`OutputArraySchema`	Mark classes than have a save() and fromDoc() function.
`InputParameter`	Define an input or output parameter to a process.
`OutputParameter`	Define an input or output parameter to a process.
`ProcessRequirement`	A process requirement declares a prerequisite that may or must be fulfilled before executing a process. See `Process.hints <#process>`__ and `Process.requirements <#process>`__.
`Process`	The base executable type in CWL is the `Process` object defined by the document. Note that the `Process` object is abstract and cannot be directly executed.
`InlineJavascriptRequirement`	Indicates that the workflow platform must support inline Javascript expressions. If this requirement is not present, the workflow platform must not perform expression interpolatation.
`SchemaDefRequirement`	This field consists of an array of type definitions which must be used when interpreting the `inputs` and `outputs` fields. When a `type` field contain a IRI, the implementation must check if the type is defined in `schemaDefs` and use that definition. If the type is not found in `schemaDefs`, it is an error. The entries in `schemaDefs` must be processed in the order listed such that later schema definitions may refer to earlier schema definitions.
`EnvironmentDef`	Define an environment variable that will be set in the runtime environment by the workflow platform when executing the command line tool. May be the result of executing an expression, such as getting a parameter from input.
`CommandLineBinding`	When listed under `inputBinding` in the input schema, the term "value" refers to the the corresponding value in the input object. For binding objects listed in `CommandLineTool.arguments`, the term "value" refers to the effective value after evaluating `valueFrom`.
`CommandOutputBinding`	Describes how to generate an output parameter based on the files produced by a CommandLineTool.
`CommandInputRecordField`	A field of a record.
`CommandInputRecordSchema`	Mark classes than have a save() and fromDoc() function.
`CommandInputEnumSchema`	Define an enumerated type.
`CommandInputArraySchema`	Mark classes than have a save() and fromDoc() function.
`CommandOutputRecordField`	A field of a record.
`CommandOutputRecordSchema`	Mark classes than have a save() and fromDoc() function.
`CommandOutputEnumSchema`	Define an enumerated type.
`CommandOutputArraySchema`	Mark classes than have a save() and fromDoc() function.
`CommandInputParameter`	An input parameter for a CommandLineTool.
`CommandOutputParameter`	An output parameter for a CommandLineTool.
`CommandLineTool`	This defines the schema of the CWL Command Line Tool Description document.
`DockerRequirement`	Indicates that a workflow component should be run in a Docker container, and specifies how to fetch or build the image.
`SoftwareRequirement`	A list of software packages that should be configured in the environment of the defined process.
`SoftwarePackage`	Mark classes than have a save() and fromDoc() function.
`Dirent`	Define a file or subdirectory that must be placed in the designated output directory prior to executing the command line tool. May be the result of executing an expression, such as building a configuration file from a template.
`InitialWorkDirRequirement`	Define a list of files and subdirectories that must be created by the workflow platform in the designated output directory prior to executing the command line tool.
`EnvVarRequirement`	Define a list of environment variables which will be set in the execution environment of the tool. See `EnvironmentDef` for details.
`ShellCommandRequirement`	Modify the behavior of CommandLineTool to generate a single string containing a shell command line. Each item in the argument list must be joined into a string separated by single spaces and quoted to prevent interpretation by the shell, unless `CommandLineBinding` for that argument contains `shellQuote: false`. If `shellQuote: false` is specified, the argument is joined into the command string without quoting, which allows the use of shell metacharacters such as `\|` for pipes.
`ResourceRequirement`	Specify basic hardware resource requirements.
`ExpressionToolOutputParameter`	Define an input or output parameter to a process.
`ExpressionTool`	Execute an expression as a Workflow step.
`WorkflowOutputParameter`	Describe an output parameter of a workflow. The parameter must be connected to one or more parameters defined in the workflow that will provide the value of the output parameter.
`Sink`	Mark classes than have a save() and fromDoc() function.
`WorkflowStepInput`	The input of a workflow step connects an upstream parameter (from the workflow inputs, or the outputs of other workflows steps) with the input parameters of the underlying step.
`WorkflowStepOutput`	Associate an output parameter of the underlying process with a workflow parameter. The workflow parameter (given in the `id` field) be may be used as a `source` to connect with input parameters of other workflow steps, or with an output parameter of the process.
`WorkflowStep`	A workflow step is an executable element of a workflow. It specifies the underlying process implementation (such as `CommandLineTool` or another `Workflow`) in the `run` field and connects the input and output parameters of the underlying process to workflow parameters.
`Workflow`	A workflow describes a set of steps and the dependencies between those steps. When a step produces output that will be consumed by a second step, the first step is a dependency of the second step.
`SubworkflowFeatureRequirement`	Indicates that the workflow platform must support nested workflows in the `run` field of WorkflowStep.
`ScatterFeatureRequirement`	Indicates that the workflow platform must support the `scatter` and `scatterMethod` fields of WorkflowStep.
`MultipleInputFeatureRequirement`	Indicates that the workflow platform must support multiple inbound data links listed in the `source` field of WorkflowStepInput.
`StepInputExpressionRequirement`	Indicate that the workflow platform must support the `valueFrom` field of WorkflowStepInput.
`LoadListingRequirement`	A process requirement declares a prerequisite that may or must be fulfilled before executing a process. See `Process.hints <#process>`__ and `Process.requirements <#process>`__.
`InplaceUpdateRequirement`	A process requirement declares a prerequisite that may or must be fulfilled before executing a process. See `Process.hints <#process>`__ and `Process.requirements <#process>`__.
`Secrets`	A process requirement declares a prerequisite that may or must be fulfilled before executing a process. See `Process.hints <#process>`__ and `Process.requirements <#process>`__.
`TimeLimit`	Set an upper limit on the execution time of a CommandLineTool or ExpressionTool. A tool execution which exceeds the time limit may be preemptively terminated and considered failed. May also be used by batch systems to make scheduling decisions.
`WorkReuse`	For implementations that support reusing output from past work (on the assumption that same code and same input produce same results), control whether to enable or disable the reuse behavior for a particular tool or step (to accommodate situations where that assumption is incorrect). A reused step is not executed but instead returns the same output as the original execution.
`NetworkAccess`	Indicate whether a process requires outgoing IPv4/IPv6 network access. Choice of IPv4 or IPv6 is implementation and site specific, correct tools must support both.
`ProcessGenerator`	The base executable type in CWL is the `Process` object defined by the document. Note that the `Process` object is abstract and cannot be directly executed.
`MPIRequirement`	Indicates that a process requires an MPI runtime.
`CUDARequirement`	Require support for NVIDA CUDA (GPU hardware acceleration).
`ShmSize`	A process requirement declares a prerequisite that may or must be fulfilled before executing a process. See `Process.hints <#process>`__ and `Process.requirements <#process>`__.

Functions

`parser_info`()
`load_document`(doc[, baseuri, loadingOptions])
`load_document_with_metadata`(doc[, baseuri, ...])
`load_document_by_string`(string, uri[, loadingOptions])
`load_document_by_yaml`(yaml, uri[, loadingOptions])	Shortcut to load via a YAML object.

Module Contents

cwl_utils.parser.cwl_v1_0.parser_info()

Return type:: str

class cwl_utils.parser.cwl_v1_0.CWLArraySchema(items, type_, extension_fields=None, loadingOptions=None)

Bases: schema_salad.metaschema.ArraySchema

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CWLArraySchema

Mark classes than have a save() and fromDoc() function.

Parameters:

items (Any)
type_ (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

items

type_

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CWLRecordField(name, type_, doc=None, extension_fields=None, loadingOptions=None)

Bases: schema_salad.metaschema.RecordField

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CWLRecordField

A field of a record.

Parameters:

name (Any)
type_ (Any)
doc (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

name: str

doc = None

type_

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CWLRecordSchema(type_, fields=None, extension_fields=None, loadingOptions=None)

Bases: schema_salad.metaschema.RecordSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CWLRecordSchema

Mark classes than have a save() and fromDoc() function.

Parameters:

type_ (Any)
fields (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

fields = None

type_

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.File(location=None, path=None, basename=None, dirname=None, nameroot=None, nameext=None, checksum=None, size=None, secondaryFiles=None, format=None, contents=None, extension_fields=None, loadingOptions=None)

Bases: schema_salad.runtime.Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_0.File

Represents a file (or group of files when secondaryFiles is provided) that will be accessible by tools using standard POSIX file system call API such as open(2) and read(2).

Files are represented as objects with class of File. File objects have a number of properties that provide metadata about the file.

The location property of a File is a URI that uniquely identifies the file. Implementations must support the file:// URI scheme and may support other schemes such as http://. The value of location may also be a relative reference, in which case it must be resolved relative to the URI of the document it appears in. Alternately to location, implementations must also accept the path property on File, which must be a filesystem path available on the same host as the CWL runner (for inputs) or the runtime environment of a command line tool execution (for command line tool outputs).

If no location or path is specified, a file object must specify contents with the UTF-8 text content of the file. This is a “file literal”. File literals do not correspond to external resources, but are created on disk with contents with when needed for a executing a tool. Where appropriate, expressions can return file literals to define new files on a runtime. The maximum size of contents is 64 kilobytes.

The basename property defines the filename on disk where the file is staged. This may differ from the resource name. If not provided, basename must be computed from the last path part of location and made available to expressions.

The secondaryFiles property is a list of File or Directory objects that must be staged in the same directory as the primary file. It is an error for file names to be duplicated in secondaryFiles.

The size property is the size in bytes of the File. It must be computed from the resource and made available to expressions. The checksum field contains a cryptographic hash of the file content for use it verifying file contents. Implementations may, at user option, enable or disable computation of the checksum field for performance or other reasons. However, the ability to compute output checksums is required to pass the CWL conformance test suite.

When executing a CommandLineTool, the files and secondary files may be staged to an arbitrary directory, but must use the value of basename for the filename. The path property must be file path in the context of the tool execution runtime (local to the compute node, or within the executing container). All computed properties should be available to expressions. File literals also must be staged and path must be set.

When collecting CommandLineTool outputs, glob matching returns file paths (with the path property) and the derived properties. This can all be modified by outputEval. Alternately, if the file cwl.output.json is present in the output, outputBinding is ignored.

File objects in the output must provide either a location URI or a path property in the context of the tool execution runtime (local to the compute node, or within the executing container).

When evaluating an ExpressionTool, file objects must be referenced via location (the expression tool does not have access to files on disk so path is meaningless) or as file literals. It is legal to return a file object with an existing location but a different basename. The loadContents field of ExpressionTool inputs behaves the same as on CommandLineTool inputs, however it is not meaningful on the outputs.

An ExpressionTool may forward file references from input to output by using the same value for location.

Parameters:

location (Any | None)
path (Any | None)
basename (Any | None)
dirname (Any | None)
nameroot (Any | None)
nameext (Any | None)
checksum (Any | None)
size (Any | None)
secondaryFiles (Any | None)
format (Any | None)
contents (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'File'

location = None

path = None

basename = None

dirname = None

nameroot = None

nameext = None

checksum = None

size = None

secondaryFiles = None

format = None

contents = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.Directory(location=None, path=None, basename=None, listing=None, extension_fields=None, loadingOptions=None)

Bases: schema_salad.runtime.Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_0.Directory

Represents a directory to present to a command line tool.

Directories are represented as objects with class of Directory. Directory objects have a number of properties that provide metadata about the directory.

The location property of a Directory is a URI that uniquely identifies the directory. Implementations must support the file:// URI scheme and may support other schemes such as http://. Alternately to location, implementations must also accept the path property on Directory, which must be a filesystem path available on the same host as the CWL runner (for inputs) or the runtime environment of a command line tool execution (for command line tool outputs).

A Directory object may have a listing field. This is a list of File and Directory objects that are contained in the Directory. For each entry in listing, the basename property defines the name of the File or Subdirectory when staged to disk. If listing is not provided, the implementation must have some way of fetching the Directory listing at runtime based on the location field.

If a Directory does not have location, it is a Directory literal. A Directory literal must provide listing. Directory literals must be created on disk at runtime as needed.

The resources in a Directory literal do not need to have any implied relationship in their location. For example, a Directory listing may contain two files located on different hosts. It is the responsibility of the runtime to ensure that those files are staged to disk appropriately. Secondary files associated with files in listing must also be staged to the same Directory.

When executing a CommandLineTool, Directories must be recursively staged first and have local values of path assigned.

Directory objects in CommandLineTool output must provide either a location URI or a path property in the context of the tool execution runtime (local to the compute node, or within the executing container).

An ExpressionTool may forward file references from input to output by using the same value for location.

Name conflicts (the same basename appearing multiple times in listing or in any entry in secondaryFiles in the listing) is a fatal error.

Parameters:

location (Any | None)
path (Any | None)
basename (Any | None)
listing (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'Directory'

location = None

path = None

basename = None

listing = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.SchemaBase

Bases: schema_salad.runtime.Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_0.SchemaBase

Mark classes than have a save() and fromDoc() function.

class cwl_utils.parser.cwl_v1_0.Parameter

Bases: SchemaBase

Inheritance diagram of cwl_utils.parser.cwl_v1_0.Parameter

Define an input or output parameter to a process.

class cwl_utils.parser.cwl_v1_0.InputBinding

Bases: schema_salad.runtime.Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_0.InputBinding

Mark classes than have a save() and fromDoc() function.

class cwl_utils.parser.cwl_v1_0.OutputBinding

Bases: schema_salad.runtime.Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_0.OutputBinding

Mark classes than have a save() and fromDoc() function.

class cwl_utils.parser.cwl_v1_0.InputSchema

Bases: SchemaBase

Inheritance diagram of cwl_utils.parser.cwl_v1_0.InputSchema

Mark classes than have a save() and fromDoc() function.

class cwl_utils.parser.cwl_v1_0.OutputSchema

Bases: SchemaBase

Inheritance diagram of cwl_utils.parser.cwl_v1_0.OutputSchema

Mark classes than have a save() and fromDoc() function.

class cwl_utils.parser.cwl_v1_0.InputRecordField(name, type_, doc=None, inputBinding=None, label=None, extension_fields=None, loadingOptions=None)

Bases: CWLRecordField

Inheritance diagram of cwl_utils.parser.cwl_v1_0.InputRecordField

A field of a record.

Parameters:

name (Any)
type_ (Any)
doc (Any | None)
inputBinding (Any | None)
label (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

name: str

doc = None

type_

inputBinding = None

label = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.InputRecordSchema(type_, fields=None, label=None, name=None, extension_fields=None, loadingOptions=None)

Bases: CWLRecordSchema, InputSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_0.InputRecordSchema

Mark classes than have a save() and fromDoc() function.

Parameters:

type_ (Any)
fields (Any | None)
label (Any | None)
name (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

name: str

fields = None

type_

label = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.InputEnumSchema(symbols, type_, name=None, label=None, inputBinding=None, extension_fields=None, loadingOptions=None)

Bases: schema_salad.metaschema.EnumSchema, InputSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_0.InputEnumSchema

Define an enumerated type.

Parameters:

symbols (Any)
type_ (Any)
name (Any | None)
label (Any | None)
inputBinding (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

name: str

symbols

type_

label = None

inputBinding = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.InputArraySchema(items, type_, label=None, inputBinding=None, extension_fields=None, loadingOptions=None)

Bases: CWLArraySchema, InputSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_0.InputArraySchema

Mark classes than have a save() and fromDoc() function.

Parameters:

items (Any)
type_ (Any)
label (Any | None)
inputBinding (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

items

type_

label = None

inputBinding = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.OutputRecordField(name, type_, doc=None, outputBinding=None, extension_fields=None, loadingOptions=None)

Bases: CWLRecordField

Inheritance diagram of cwl_utils.parser.cwl_v1_0.OutputRecordField

A field of a record.

Parameters:

name (Any)
type_ (Any)
doc (Any | None)
outputBinding (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

name: str

doc = None

type_

outputBinding = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.OutputRecordSchema(type_, fields=None, label=None, extension_fields=None, loadingOptions=None)

Bases: CWLRecordSchema, OutputSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_0.OutputRecordSchema

Mark classes than have a save() and fromDoc() function.

Parameters:

type_ (Any)
fields (Any | None)
label (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

fields = None

type_

label = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.OutputEnumSchema(symbols, type_, name=None, label=None, outputBinding=None, extension_fields=None, loadingOptions=None)

Bases: schema_salad.metaschema.EnumSchema, OutputSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_0.OutputEnumSchema

Define an enumerated type.

Parameters:

symbols (Any)
type_ (Any)
name (Any | None)
label (Any | None)
outputBinding (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

name: str

symbols

type_

label = None

outputBinding = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.OutputArraySchema(items, type_, label=None, outputBinding=None, extension_fields=None, loadingOptions=None)

Bases: CWLArraySchema, OutputSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_0.OutputArraySchema

Mark classes than have a save() and fromDoc() function.

Parameters:

items (Any)
type_ (Any)
label (Any | None)
outputBinding (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

items

type_

label = None

outputBinding = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.InputParameter(id, label=None, secondaryFiles=None, streamable=None, doc=None, format=None, inputBinding=None, default=None, type_=None, extension_fields=None, loadingOptions=None)

Bases: Parameter

Inheritance diagram of cwl_utils.parser.cwl_v1_0.InputParameter

Define an input or output parameter to a process.

Parameters:

id (Any)
label (Any | None)
secondaryFiles (Any | None)
streamable (Any | None)
doc (Any | None)
format (Any | None)
inputBinding (Any | None)
default (Any | None)
type_ (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

id: str

label = None

secondaryFiles = None

streamable = None

doc = None

format = None

inputBinding = None

default = None

type_ = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.OutputParameter(id, label=None, secondaryFiles=None, streamable=None, doc=None, outputBinding=None, format=None, extension_fields=None, loadingOptions=None)

Bases: Parameter

Inheritance diagram of cwl_utils.parser.cwl_v1_0.OutputParameter

Define an input or output parameter to a process.

Parameters:

id (Any)
label (Any | None)
secondaryFiles (Any | None)
streamable (Any | None)
doc (Any | None)
outputBinding (Any | None)
format (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

id: str

label = None

secondaryFiles = None

streamable = None

doc = None

outputBinding = None

format = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.ProcessRequirement

Bases: schema_salad.runtime.Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_0.ProcessRequirement

A process requirement declares a prerequisite that may or must be fulfilled before executing a process. See `Process.hints <#process>`__ and `Process.requirements <#process>`__.

Process requirements are the primary mechanism for specifying extensions to the CWL core specification.

class cwl_utils.parser.cwl_v1_0.Process

Bases: schema_salad.runtime.Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_0.Process

The base executable type in CWL is the Process object defined by the document. Note that the Process object is abstract and cannot be directly executed.

class cwl_utils.parser.cwl_v1_0.InlineJavascriptRequirement(expressionLib=None, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.InlineJavascriptRequirement

Indicates that the workflow platform must support inline Javascript expressions. If this requirement is not present, the workflow platform must not perform expression interpolatation.

Parameters:

expressionLib (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'InlineJavascriptRequirement'

expressionLib = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.SchemaDefRequirement(types, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.SchemaDefRequirement

This field consists of an array of type definitions which must be used when interpreting the inputs and outputs fields. When a type field contain a IRI, the implementation must check if the type is defined in schemaDefs and use that definition. If the type is not found in schemaDefs, it is an error. The entries in schemaDefs must be processed in the order listed such that later schema definitions may refer to earlier schema definitions.

Parameters:

types (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'SchemaDefRequirement'

types

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.EnvironmentDef(envName, envValue, extension_fields=None, loadingOptions=None)

Bases: schema_salad.runtime.Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_0.EnvironmentDef

Define an environment variable that will be set in the runtime environment by the workflow platform when executing the command line tool. May be the result of executing an expression, such as getting a parameter from input.

Parameters:

envName (Any)
envValue (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

envName

envValue

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CommandLineBinding(loadContents=None, position=None, prefix=None, separate=None, itemSeparator=None, valueFrom=None, shellQuote=None, extension_fields=None, loadingOptions=None)

Bases: InputBinding

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CommandLineBinding

When listed under inputBinding in the input schema, the term “value” refers to the the corresponding value in the input object. For binding objects listed in CommandLineTool.arguments, the term “value” refers to the effective value after evaluating valueFrom.

The binding behavior when building the command line depends on the data type of the value. If there is a mismatch between the type described by the input schema and the effective value, such as resulting from an expression evaluation, an implementation must use the data type of the effective value.

string: Add prefix and the string to the command line.
number: Add prefix and decimal representation to command line.
boolean: If true, add prefix to the command line. If false, add nothing.
File: Add prefix and the value of `File.path <#File>`__ to the command line.
Directory: Add prefix and the value of `Directory.path <#Directory>`__ to the command line.
array: If itemSeparator is specified, add prefix and the join the array into a single string with itemSeparator separating the items. Otherwise first add prefix, then recursively process individual elements. If the array is empty, it does not add anything to command line.
object: Add prefix only, and recursively add object fields for which inputBinding is specified.
null: Add nothing.

Parameters:

loadContents (Any | None)
position (Any | None)
prefix (Any | None)
separate (Any | None)
itemSeparator (Any | None)
valueFrom (Any | None)
shellQuote (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

loadContents = None

position = None

prefix = None

separate = None

itemSeparator = None

valueFrom = None

shellQuote = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CommandOutputBinding(glob=None, loadContents=None, outputEval=None, extension_fields=None, loadingOptions=None)

Bases: OutputBinding

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CommandOutputBinding

Describes how to generate an output parameter based on the files produced by a CommandLineTool.

The output parameter value is generated by applying these operations in the following order:

glob
loadContents
outputEval
secondaryFiles

Parameters:

glob (Any | None)
loadContents (Any | None)
outputEval (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

glob = None

loadContents = None

outputEval = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CommandInputRecordField(name, type_, doc=None, inputBinding=None, label=None, extension_fields=None, loadingOptions=None)

Bases: InputRecordField

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CommandInputRecordField

A field of a record.

Parameters:

name (Any)
type_ (Any)
doc (Any | None)
inputBinding (Any | None)
label (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

name: str

doc = None

type_

inputBinding = None

label = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CommandInputRecordSchema(type_, fields=None, label=None, name=None, extension_fields=None, loadingOptions=None)

Bases: InputRecordSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CommandInputRecordSchema

Mark classes than have a save() and fromDoc() function.

Parameters:

type_ (Any)
fields (Any | None)
label (Any | None)
name (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

name: str

fields = None

type_

label = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CommandInputEnumSchema(symbols, type_, name=None, label=None, inputBinding=None, extension_fields=None, loadingOptions=None)

Bases: InputEnumSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CommandInputEnumSchema

Define an enumerated type.

Parameters:

symbols (Any)
type_ (Any)
name (Any | None)
label (Any | None)
inputBinding (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

name: str

symbols

type_

label = None

inputBinding = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CommandInputArraySchema(items, type_, label=None, inputBinding=None, extension_fields=None, loadingOptions=None)

Bases: InputArraySchema

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CommandInputArraySchema

Mark classes than have a save() and fromDoc() function.

Parameters:

items (Any)
type_ (Any)
label (Any | None)
inputBinding (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

items

type_

label = None

inputBinding = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CommandOutputRecordField(name, type_, doc=None, outputBinding=None, extension_fields=None, loadingOptions=None)

Bases: OutputRecordField

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CommandOutputRecordField

A field of a record.

Parameters:

name (Any)
type_ (Any)
doc (Any | None)
outputBinding (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

name: str

doc = None

type_

outputBinding = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CommandOutputRecordSchema(type_, fields=None, label=None, name=None, extension_fields=None, loadingOptions=None)

Bases: OutputRecordSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CommandOutputRecordSchema

Mark classes than have a save() and fromDoc() function.

Parameters:

type_ (Any)
fields (Any | None)
label (Any | None)
name (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

name: str

fields = None

type_

label = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CommandOutputEnumSchema(symbols, type_, name=None, label=None, outputBinding=None, extension_fields=None, loadingOptions=None)

Bases: OutputEnumSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CommandOutputEnumSchema

Define an enumerated type.

Parameters:

symbols (Any)
type_ (Any)
name (Any | None)
label (Any | None)
outputBinding (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

name: str

symbols

type_

label = None

outputBinding = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CommandOutputArraySchema(items, type_, label=None, outputBinding=None, extension_fields=None, loadingOptions=None)

Bases: OutputArraySchema

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CommandOutputArraySchema

Mark classes than have a save() and fromDoc() function.

Parameters:

items (Any)
type_ (Any)
label (Any | None)
outputBinding (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

items

type_

label = None

outputBinding = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CommandInputParameter(id, label=None, secondaryFiles=None, streamable=None, doc=None, format=None, inputBinding=None, default=None, type_=None, extension_fields=None, loadingOptions=None)

Bases: InputParameter

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CommandInputParameter

An input parameter for a CommandLineTool.

Parameters:

id (Any)
label (Any | None)
secondaryFiles (Any | None)
streamable (Any | None)
doc (Any | None)
format (Any | None)
inputBinding (Any | None)
default (Any | None)
type_ (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

id: str

label = None

secondaryFiles = None

streamable = None

doc = None

format = None

inputBinding = None

default = None

type_ = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CommandOutputParameter(id, label=None, secondaryFiles=None, streamable=None, doc=None, outputBinding=None, format=None, type_=None, extension_fields=None, loadingOptions=None)

Bases: OutputParameter

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CommandOutputParameter

An output parameter for a CommandLineTool.

Parameters:

id (Any)
label (Any | None)
secondaryFiles (Any | None)
streamable (Any | None)
doc (Any | None)
outputBinding (Any | None)
format (Any | None)
type_ (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

id: str

label = None

secondaryFiles = None

streamable = None

doc = None

outputBinding = None

format = None

type_ = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CommandLineTool(inputs, outputs, id=None, requirements=None, hints=None, label=None, doc=None, cwlVersion=None, baseCommand=None, arguments=None, stdin=None, stderr=None, stdout=None, successCodes=None, temporaryFailCodes=None, permanentFailCodes=None, extension_fields=None, loadingOptions=None)

Bases: Process

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CommandLineTool

This defines the schema of the CWL Command Line Tool Description document.

Parameters:

inputs (Any)
outputs (Any)
id (Any | None)
requirements (Any | None)
hints (Any | None)
label (Any | None)
doc (Any | None)
cwlVersion (Any | None)
baseCommand (Any | None)
arguments (Any | None)
stdin (Any | None)
stderr (Any | None)
stdout (Any | None)
successCodes (Any | None)
temporaryFailCodes (Any | None)
permanentFailCodes (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

id: str

inputs

outputs

requirements = None

hints = None

label = None

doc = None

cwlVersion = None

class_: Final[str] = 'CommandLineTool'

baseCommand = None

arguments = None

stdin = None

stderr = None

stdout = None

successCodes = None

temporaryFailCodes = None

permanentFailCodes = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.DockerRequirement(dockerPull=None, dockerLoad=None, dockerFile=None, dockerImport=None, dockerImageId=None, dockerOutputDirectory=None, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.DockerRequirement

Indicates that a workflow component should be run in a Docker container, and specifies how to fetch or build the image.

If a CommandLineTool lists DockerRequirement under hints (or requirements), it may (or must) be run in the specified Docker container.

The platform must first acquire or install the correct Docker image as specified by dockerPull, dockerImport, dockerLoad or dockerFile.

The platform must execute the tool in the container using docker run with the appropriate Docker image and tool command line.

The workflow platform may provide input files and the designated output directory through the use of volume bind mounts. The platform should rewrite file paths in the input object to correspond to the Docker bind mounted locations. That is, the platform should rewrite values in the parameter context such as runtime.outdir, runtime.tmpdir and others to be valid paths within the container.

When running a tool contained in Docker, the workflow platform must not assume anything about the contents of the Docker container, such as the presence or absence of specific software, except to assume that the generated command line represents a valid command within the runtime environment of the container.

Interaction with other requirements

If EnvVarRequirement is specified alongside a DockerRequirement, the environment variables must be provided to Docker using --env or --env-file and interact with the container’s preexisting environment as defined by Docker.

class_: Final[str] = 'DockerRequirement'

dockerPull = None

dockerLoad = None

dockerFile = None

dockerImport = None

dockerImageId = None

dockerOutputDirectory = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

Parameters:

dockerPull (Any | None)
dockerLoad (Any | None)
dockerFile (Any | None)
dockerImport (Any | None)
dockerImageId (Any | None)
dockerOutputDirectory (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class cwl_utils.parser.cwl_v1_0.SoftwareRequirement(packages, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.SoftwareRequirement

A list of software packages that should be configured in the environment of the defined process.

Parameters:

packages (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'SoftwareRequirement'

packages

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.SoftwarePackage(package, version=None, specs=None, extension_fields=None, loadingOptions=None)

Bases: schema_salad.runtime.Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_0.SoftwarePackage

Mark classes than have a save() and fromDoc() function.

Parameters:

package (Any)
version (Any | None)
specs (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

package

version = None

specs = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.Dirent(entry, entryname=None, writable=None, extension_fields=None, loadingOptions=None)

Bases: schema_salad.runtime.Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_0.Dirent

Define a file or subdirectory that must be placed in the designated output directory prior to executing the command line tool. May be the result of executing an expression, such as building a configuration file from a template.

Parameters:

entry (Any)
entryname (Any | None)
writable (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

entryname = None

entry

writable = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.InitialWorkDirRequirement(listing, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.InitialWorkDirRequirement

Define a list of files and subdirectories that must be created by the workflow platform in the designated output directory prior to executing the command line tool.

Parameters:

listing (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'InitialWorkDirRequirement'

listing

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.EnvVarRequirement(envDef, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.EnvVarRequirement

Define a list of environment variables which will be set in the execution environment of the tool. See EnvironmentDef for details.

Parameters:

envDef (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'EnvVarRequirement'

envDef

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.ShellCommandRequirement(extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.ShellCommandRequirement

Modify the behavior of CommandLineTool to generate a single string containing a shell command line. Each item in the argument list must be joined into a string separated by single spaces and quoted to prevent interpretation by the shell, unless CommandLineBinding for that argument contains shellQuote: false. If shellQuote: false is specified, the argument is joined into the command string without quoting, which allows the use of shell metacharacters such as | for pipes.

Parameters:

extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'ShellCommandRequirement'

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.ResourceRequirement(coresMin=None, coresMax=None, ramMin=None, ramMax=None, tmpdirMin=None, tmpdirMax=None, outdirMin=None, outdirMax=None, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.ResourceRequirement

Specify basic hardware resource requirements.

“min” is the minimum amount of a resource that must be reserved to schedule a job. If “min” cannot be satisfied, the job should not be run.

“max” is the maximum amount of a resource that the job shall be permitted to use. If a node has sufficient resources, multiple jobs may be scheduled on a single node provided each job’s “max” resource requirements are met. If a job attempts to exceed its “max” resource allocation, an implementation may deny additional resources, which may result in job failure.

If “min” is specified but “max” is not, then “max” == “min” If “max” is specified by “min” is not, then “min” == “max”.

It is an error if max < min.

It is an error if the value of any of these fields is negative.

If neither “min” nor “max” is specified for a resource, an implementation may provide a default.

Parameters:

coresMin (Any | None)
coresMax (Any | None)
ramMin (Any | None)
ramMax (Any | None)
tmpdirMin (Any | None)
tmpdirMax (Any | None)
outdirMin (Any | None)
outdirMax (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'ResourceRequirement'

coresMin = None

coresMax = None

ramMin = None

ramMax = None

tmpdirMin = None

tmpdirMax = None

outdirMin = None

outdirMax = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.ExpressionToolOutputParameter(id, label=None, secondaryFiles=None, streamable=None, doc=None, outputBinding=None, format=None, type_=None, extension_fields=None, loadingOptions=None)

Bases: OutputParameter

Inheritance diagram of cwl_utils.parser.cwl_v1_0.ExpressionToolOutputParameter

Define an input or output parameter to a process.

Parameters:

id (Any)
label (Any | None)
secondaryFiles (Any | None)
streamable (Any | None)
doc (Any | None)
outputBinding (Any | None)
format (Any | None)
type_ (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

id: str

label = None

secondaryFiles = None

streamable = None

doc = None

outputBinding = None

format = None

type_ = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.ExpressionTool(inputs, outputs, expression, id=None, requirements=None, hints=None, label=None, doc=None, cwlVersion=None, extension_fields=None, loadingOptions=None)

Bases: Process

Inheritance diagram of cwl_utils.parser.cwl_v1_0.ExpressionTool

Execute an expression as a Workflow step.

Parameters:

inputs (Any)
outputs (Any)
expression (Any)
id (Any | None)
requirements (Any | None)
hints (Any | None)
label (Any | None)
doc (Any | None)
cwlVersion (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

id: str

inputs

outputs

requirements = None

hints = None

label = None

doc = None

cwlVersion = None

class_: Final[str] = 'ExpressionTool'

expression

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.WorkflowOutputParameter(id, label=None, secondaryFiles=None, streamable=None, doc=None, outputBinding=None, format=None, outputSource=None, linkMerge=None, type_=None, extension_fields=None, loadingOptions=None)

Bases: OutputParameter

Inheritance diagram of cwl_utils.parser.cwl_v1_0.WorkflowOutputParameter

Describe an output parameter of a workflow. The parameter must be connected to one or more parameters defined in the workflow that will provide the value of the output parameter.

Parameters:

id (Any)
label (Any | None)
secondaryFiles (Any | None)
streamable (Any | None)
doc (Any | None)
outputBinding (Any | None)
format (Any | None)
outputSource (Any | None)
linkMerge (Any | None)
type_ (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

id: str

label = None

secondaryFiles = None

streamable = None

doc = None

outputBinding = None

format = None

outputSource = None

linkMerge = None

type_ = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.Sink

Bases: schema_salad.runtime.Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_0.Sink

Mark classes than have a save() and fromDoc() function.

class cwl_utils.parser.cwl_v1_0.WorkflowStepInput(id, source=None, linkMerge=None, default=None, valueFrom=None, extension_fields=None, loadingOptions=None)

Bases: Sink

Inheritance diagram of cwl_utils.parser.cwl_v1_0.WorkflowStepInput

The input of a workflow step connects an upstream parameter (from the workflow inputs, or the outputs of other workflows steps) with the input parameters of the underlying step.

Input object

A WorkflowStepInput object must contain an id field in the form #fieldname or #prefix/fieldname. When the id field contains a slash / the field name consists of the characters following the final slash (the prefix portion may contain one or more slashes to indicate scope). This defines a field of the workflow step input object with the value of the source parameter(s).

Merging

To merge multiple inbound data links, MultipleInputFeatureRequirement must be specified in the workflow or workflow step requirements.

If the sink parameter is an array, or named in a workflow scatter operation, there may be multiple inbound data links listed in the source field. The values from the input links are merged depending on the method specified in the linkMerge field. If not specified, the default method is “merge_nested”.

merge_nested

The input must be an array consisting of exactly one entry for each input link. If “merge_nested” is specified with a single link, the value from the link must be wrapped in a single-item list.
merge_flattened
1. The source and sink parameters must be compatible types, or the source type must be compatible with single element from the “items” type of the destination array parameter.
2. Source parameters which are arrays are concatenated. Source parameters which are single element types are appended as single elements.

id: str

source = None

linkMerge = None

default = None

valueFrom = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

Parameters:

id (Any)
source (Any | None)
linkMerge (Any | None)
default (Any | None)
valueFrom (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class cwl_utils.parser.cwl_v1_0.WorkflowStepOutput(id, extension_fields=None, loadingOptions=None)

Bases: schema_salad.runtime.Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_0.WorkflowStepOutput

Associate an output parameter of the underlying process with a workflow parameter. The workflow parameter (given in the id field) be may be used as a source to connect with input parameters of other workflow steps, or with an output parameter of the process.

Parameters:

id (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

id: str

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.WorkflowStep(id, in_, out, run, requirements=None, hints=None, label=None, doc=None, scatter=None, scatterMethod=None, extension_fields=None, loadingOptions=None)

Bases: schema_salad.runtime.Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_0.WorkflowStep

A workflow step is an executable element of a workflow. It specifies the underlying process implementation (such as CommandLineTool or another Workflow) in the run field and connects the input and output parameters of the underlying process to workflow parameters.

Scatter/gather

To use scatter/gather, ScatterFeatureRequirement must be specified in the workflow or workflow step requirements.

A “scatter” operation specifies that the associated workflow step or subworkflow should execute separately over a list of input elements. Each job making up a scatter operation is independent and may be executed concurrently.

The scatter field specifies one or more input parameters which will be scattered. An input parameter may be listed more than once. The declared type of each input parameter is implicitly becomes an array of items of the input parameter type. If a parameter is listed more than once, it becomes a nested array. As a result, upstream parameters which are connected to scattered parameters must be arrays.

All output parameter types are also implicitly wrapped in arrays. Each job in the scatter results in an entry in the output array.

If any scattered parameter runtime value is an empty array, all outputs are set to empty arrays and no work is done for the step, according to applicable scattering rules.

If scatter declares more than one input parameter, scatterMethod describes how to decompose the input into a discrete set of jobs.

dotproduct specifies that each of the input arrays are aligned and one element taken from each array to construct each job. It is an error if all input arrays are not the same length.
nested_crossproduct specifies the Cartesian product of the inputs, producing a job for every combination of the scattered inputs. The output must be nested arrays for each level of scattering, in the order that the input arrays are listed in the scatter field.
flat_crossproduct specifies the Cartesian product of the inputs, producing a job for every combination of the scattered inputs. The output arrays must be flattened to a single level, but otherwise listed in the order that the input arrays are listed in the scatter field.

Subworkflows

To specify a nested workflow as part of a workflow step, SubworkflowFeatureRequirement must be specified in the workflow or workflow step requirements.

It is a fatal error if a workflow directly or indirectly invokes itself as a subworkflow (recursive workflows are not allowed).

id: str

in_

out

requirements = None

hints = None

label = None

doc = None

run

scatter = None

scatterMethod = None

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

Parameters:

id (Any)
in_ (Any)
out (Any)
run (Any)
requirements (Any | None)
hints (Any | None)
label (Any | None)
doc (Any | None)
scatter (Any | None)
scatterMethod (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class cwl_utils.parser.cwl_v1_0.Workflow(inputs, outputs, steps, id=None, requirements=None, hints=None, label=None, doc=None, cwlVersion=None, extension_fields=None, loadingOptions=None)

Bases: Process

Inheritance diagram of cwl_utils.parser.cwl_v1_0.Workflow

A workflow describes a set of steps and the dependencies between those steps. When a step produces output that will be consumed by a second step, the first step is a dependency of the second step.

When there is a dependency, the workflow engine must execute the preceding step and wait for it to successfully produce output before executing the dependent step. If two steps are defined in the workflow graph that are not directly or indirectly dependent, these steps are independent, and may execute in any order or execute concurrently. A workflow is complete when all steps have been executed.

Dependencies between parameters are expressed using the source field on workflow step input parameters and workflow output parameters.

The source field expresses the dependency of one parameter on another such that when a value is associated with the parameter specified by source, that value is propagated to the destination parameter. When all data links inbound to a given step are fulfilled, the step is ready to execute.

Workflow success and failure

A completed step must result in one of success, temporaryFailure or permanentFailure states. An implementation may choose to retry a step execution which resulted in temporaryFailure. An implementation may choose to either continue running other steps of a workflow, or terminate immediately upon permanentFailure.

If any step of a workflow execution results in permanentFailure, then the workflow status is permanentFailure.
If one or more steps result in temporaryFailure and all other steps complete success or are not executed, then the workflow status is temporaryFailure.
If all workflow steps are executed and complete with success, then the workflow status is success.

Extensions

ScatterFeatureRequirement and SubworkflowFeatureRequirement are available as standard extensions to core workflow semantics.

id: str

inputs

outputs

requirements = None

hints = None

label = None

doc = None

cwlVersion = None

class_: Final[str] = 'Workflow'

steps

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

Parameters:

inputs (Any)
outputs (Any)
steps (Any)
id (Any | None)
requirements (Any | None)
hints (Any | None)
label (Any | None)
doc (Any | None)
cwlVersion (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class cwl_utils.parser.cwl_v1_0.SubworkflowFeatureRequirement(extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.SubworkflowFeatureRequirement

Indicates that the workflow platform must support nested workflows in the run field of WorkflowStep.

Parameters:

extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'SubworkflowFeatureRequirement'

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.ScatterFeatureRequirement(extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.ScatterFeatureRequirement

Indicates that the workflow platform must support the scatter and scatterMethod fields of WorkflowStep.

Parameters:

extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'ScatterFeatureRequirement'

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.MultipleInputFeatureRequirement(extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.MultipleInputFeatureRequirement

Indicates that the workflow platform must support multiple inbound data links listed in the source field of WorkflowStepInput.

Parameters:

extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'MultipleInputFeatureRequirement'

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.StepInputExpressionRequirement(extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.StepInputExpressionRequirement

Indicate that the workflow platform must support the valueFrom field of WorkflowStepInput.

Parameters:

extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'StepInputExpressionRequirement'

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.LoadListingRequirement(loadListing, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.LoadListingRequirement

A process requirement declares a prerequisite that may or must be fulfilled before executing a process. See `Process.hints <#process>`__ and `Process.requirements <#process>`__.

Process requirements are the primary mechanism for specifying extensions to the CWL core specification.

Parameters:

loadListing (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'LoadListingRequirement'

loadListing

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.InplaceUpdateRequirement(inplaceUpdate, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.InplaceUpdateRequirement

A process requirement declares a prerequisite that may or must be fulfilled before executing a process. See `Process.hints <#process>`__ and `Process.requirements <#process>`__.

Process requirements are the primary mechanism for specifying extensions to the CWL core specification.

Parameters:

inplaceUpdate (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'InplaceUpdateRequirement'

inplaceUpdate

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.Secrets(secrets, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.Secrets

A process requirement declares a prerequisite that may or must be fulfilled before executing a process. See `Process.hints <#process>`__ and `Process.requirements <#process>`__.

Process requirements are the primary mechanism for specifying extensions to the CWL core specification.

Parameters:

secrets (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'Secrets'

secrets

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.TimeLimit(timelimit, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.TimeLimit

Set an upper limit on the execution time of a CommandLineTool or ExpressionTool. A tool execution which exceeds the time limit may be preemptively terminated and considered failed. May also be used by batch systems to make scheduling decisions.

Parameters:

timelimit (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'TimeLimit'

timelimit

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.WorkReuse(enableReuse, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.WorkReuse

For implementations that support reusing output from past work (on the assumption that same code and same input produce same results), control whether to enable or disable the reuse behavior for a particular tool or step (to accommodate situations where that assumption is incorrect). A reused step is not executed but instead returns the same output as the original execution.

If enableReuse is not specified, correct tools should assume it is enabled by default.

Parameters:

enableReuse (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'WorkReuse'

enableReuse

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.NetworkAccess(networkAccess, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.NetworkAccess

Indicate whether a process requires outgoing IPv4/IPv6 network access. Choice of IPv4 or IPv6 is implementation and site specific, correct tools must support both.

If networkAccess is false or not specified, tools must not assume network access, except for localhost (the loopback device).

If networkAccess is true, the tool must be able to make outgoing connections to network resources. Resources may be on a private subnet or the public Internet. However, implementations and sites may apply their own security policies to restrict what is accessible by the tool.

Enabling network access does not imply a publicly routable IP address or the ability to accept inbound connections.

Parameters:

networkAccess (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'NetworkAccess'

networkAccess

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.ProcessGenerator(inputs, outputs, run, id=None, requirements=None, hints=None, label=None, doc=None, cwlVersion=None, extension_fields=None, loadingOptions=None)

Bases: Process

Inheritance diagram of cwl_utils.parser.cwl_v1_0.ProcessGenerator

The base executable type in CWL is the Process object defined by the document. Note that the Process object is abstract and cannot be directly executed.

Parameters:

inputs (Any)
outputs (Any)
run (Any)
id (Any | None)
requirements (Any | None)
hints (Any | None)
label (Any | None)
doc (Any | None)
cwlVersion (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

id: str

inputs

outputs

requirements = None

hints = None

label = None

doc = None

cwlVersion = None

class_: Final[str] = 'ProcessGenerator'

run

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.MPIRequirement(processes, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.MPIRequirement

Indicates that a process requires an MPI runtime.

Parameters:

processes (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'MPIRequirement'

processes

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.CUDARequirement(cudaComputeCapability, cudaVersionMin, cudaDeviceCountMax=None, cudaDeviceCountMin=None, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.CUDARequirement

Require support for NVIDA CUDA (GPU hardware acceleration).

Parameters:

cudaComputeCapability (Any)
cudaVersionMin (Any)
cudaDeviceCountMax (Any | None)
cudaDeviceCountMin (Any | None)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'CUDARequirement'

cudaComputeCapability

cudaDeviceCountMax = None

cudaDeviceCountMin = None

cudaVersionMin

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

class cwl_utils.parser.cwl_v1_0.ShmSize(shmSize, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_0.ShmSize

A process requirement declares a prerequisite that may or must be fulfilled before executing a process. See `Process.hints <#process>`__ and `Process.requirements <#process>`__.

Process requirements are the primary mechanism for specifying extensions to the CWL core specification.

Parameters:

shmSize (Any)
extension_fields (collections.abc.MutableMapping[str, Any] | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

class_: Final[str] = 'ShmSize'

shmSize

__eq__(other)

Parameters:: other (Any)
Return type:: bool

__hash__()

Return type:: int

classmethod fromDoc(doc, baseuri, loadingOptions, docRoot=None)

Construct this object from the result of yaml.load().

Parameters:

doc (Any)
baseuri (str)
loadingOptions (schema_salad.runtime.LoadingOptions)
docRoot (str | None)

Return type:

Self

save(top=False, base_url='', relative_uris=True)

Convert this object to a JSON/YAML friendly dictionary.

Parameters:

top (bool)
base_url (str)
relative_uris (bool)

Return type:

dict[str, Any]

attrs: ClassVar[collections.abc.Collection[str]]

cwl_utils.parser.cwl_v1_0.strtype: Final

cwl_utils.parser.cwl_v1_0.inttype: Final

cwl_utils.parser.cwl_v1_0.floattype: Final

cwl_utils.parser.cwl_v1_0.booltype: Final

cwl_utils.parser.cwl_v1_0.None_type: Final

cwl_utils.parser.cwl_v1_0.Any_type: Final

cwl_utils.parser.cwl_v1_0.DocumentedProxyLoader: Final

cwl_utils.parser.cwl_v1_0.PrimitiveTypeLoader: Final

Names of salad data types (based on Avro schema declarations).

Refer to the Avro schema declaration documentation for detailed information.

null: no value

boolean: a binary value

int: 32-bit signed integer

long: 64-bit signed integer

float: single precision (32-bit) IEEE 754 floating-point number

double: double precision (64-bit) IEEE 754 floating-point number

string: Unicode character sequence

cwl_utils.parser.cwl_v1_0.AnyLoader: Final: The Any type validates for any non-null value.

cwl_utils.parser.cwl_v1_0.RecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.RecordSchemaLoader: Final

cwl_utils.parser.cwl_v1_0.EnumSchemaLoader: Final

cwl_utils.parser.cwl_v1_0.ArraySchemaLoader: Final

cwl_utils.parser.cwl_v1_0.MapSchemaLoader: Final

cwl_utils.parser.cwl_v1_0.UnionSchemaLoader: Final

cwl_utils.parser.cwl_v1_0.CWLTypeLoader: Final

Extends primitive types with the concept of a file and directory as a builtin type.

File: A File object

Directory: A Directory object

cwl_utils.parser.cwl_v1_0.CWLArraySchemaLoader: Final

cwl_utils.parser.cwl_v1_0.CWLRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.CWLRecordSchemaLoader: Final

cwl_utils.parser.cwl_v1_0.FileLoader: Final

cwl_utils.parser.cwl_v1_0.DirectoryLoader: Final

cwl_utils.parser.cwl_v1_0.CWLObjectTypeLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_CWLObjectTypeLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_union_of_None_type_or_CWLObjectTypeLoader: Final

cwl_utils.parser.cwl_v1_0.map_of_union_of_None_type_or_CWLObjectTypeLoader: Final

cwl_utils.parser.cwl_v1_0.CWLInputFileLoader: Final

cwl_utils.parser.cwl_v1_0.CWLVersionLoader: Final: Current version symbol for CWL documents.

cwl_utils.parser.cwl_v1_0.SchemaBaseProxyLoader: Final

cwl_utils.parser.cwl_v1_0.ParameterProxyLoader: Final

cwl_utils.parser.cwl_v1_0.ExpressionLoader: Final

cwl_utils.parser.cwl_v1_0.InputBindingProxyLoader: Final

cwl_utils.parser.cwl_v1_0.OutputBindingProxyLoader: Final

cwl_utils.parser.cwl_v1_0.InputSchemaProxyLoader: Final

cwl_utils.parser.cwl_v1_0.OutputSchemaProxyLoader: Final

cwl_utils.parser.cwl_v1_0.InputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.InputRecordSchemaLoader: Final

cwl_utils.parser.cwl_v1_0.InputEnumSchemaLoader: Final

cwl_utils.parser.cwl_v1_0.InputArraySchemaLoader: Final

cwl_utils.parser.cwl_v1_0.InputParameterTypeLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.OutputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.OutputRecordSchemaLoader: Final

cwl_utils.parser.cwl_v1_0.OutputEnumSchemaLoader: Final

cwl_utils.parser.cwl_v1_0.OutputArraySchemaLoader: Final

cwl_utils.parser.cwl_v1_0.OutputParameterTypeLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.InputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.OutputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.ProcessRequirementProxyLoader: Final

cwl_utils.parser.cwl_v1_0.ProcessProxyLoader: Final

cwl_utils.parser.cwl_v1_0.InlineJavascriptRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.SchemaDefRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.EnvironmentDefLoader: Final

cwl_utils.parser.cwl_v1_0.CommandLineBindingLoader: Final

cwl_utils.parser.cwl_v1_0.CommandOutputBindingLoader: Final

cwl_utils.parser.cwl_v1_0.CommandInputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.CommandInputRecordSchemaLoader: Final

cwl_utils.parser.cwl_v1_0.CommandInputEnumSchemaLoader: Final

cwl_utils.parser.cwl_v1_0.CommandInputArraySchemaLoader: Final

cwl_utils.parser.cwl_v1_0.CommandOutputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.CommandOutputRecordSchemaLoader: Final

cwl_utils.parser.cwl_v1_0.CommandOutputEnumSchemaLoader: Final

cwl_utils.parser.cwl_v1_0.CommandOutputArraySchemaLoader: Final

cwl_utils.parser.cwl_v1_0.CommandInputParameterTypeLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.CommandInputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.stdoutLoader: Final

Only valid as a type for a CommandLineTool output with no outputBinding set.

The following

outputs:
  an_output_name:
    type: stdout

stdout: a_stdout_file

is equivalent to

outputs:
  an_output_name:
    type: File
    streamable: true
    outputBinding:
      glob: a_stdout_file

stdout: a_stdout_file

If there is no stdout name provided, a random filename will be created. For example, the following

outputs:
  an_output_name:
    type: stdout

is equivalent to

outputs:
  an_output_name:
    type: File
    streamable: true
    outputBinding:
      glob: random_stdout_filenameABCDEFG

stdout: random_stdout_filenameABCDEFG

cwl_utils.parser.cwl_v1_0.stderrLoader: Final

Only valid as a type for a CommandLineTool output with no outputBinding set.

The following

outputs:
  an_output_name:
  type: stderr

stderr: a_stderr_file

is equivalent to

outputs:
  an_output_name:
    type: File
    streamable: true
    outputBinding:
      glob: a_stderr_file

stderr: a_stderr_file

If there is no stderr name provided, a random filename will be created. For example, the following

outputs:
  an_output_name:
    type: stderr

is equivalent to

outputs:
  an_output_name:
    type: File
    streamable: true
    outputBinding:
      glob: random_stderr_filenameABCDEFG

stderr: random_stderr_filenameABCDEFG

cwl_utils.parser.cwl_v1_0.CommandOutputParameterTypeLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.CommandOutputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.CommandLineToolLoader: Final

cwl_utils.parser.cwl_v1_0.DockerRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.SoftwareRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.SoftwarePackageLoader: Final

cwl_utils.parser.cwl_v1_0.DirentLoader: Final

cwl_utils.parser.cwl_v1_0.InitialWorkDirRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.EnvVarRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.ShellCommandRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.ResourceRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.ExpressionToolOutputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.ExpressionToolLoader: Final

cwl_utils.parser.cwl_v1_0.LinkMergeMethodLoader: Final: The input link merge method, described in WorkflowStepInput.

cwl_utils.parser.cwl_v1_0.WorkflowOutputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.SinkProxyLoader: Final

cwl_utils.parser.cwl_v1_0.WorkflowStepInputLoader: Final

cwl_utils.parser.cwl_v1_0.WorkflowStepOutputLoader: Final

cwl_utils.parser.cwl_v1_0.ScatterMethodLoader: Final: The scatter method, as described in workflow step scatter.

cwl_utils.parser.cwl_v1_0.WorkflowStepLoader: Final

cwl_utils.parser.cwl_v1_0.WorkflowLoader: Final

cwl_utils.parser.cwl_v1_0.SubworkflowFeatureRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.ScatterFeatureRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.MultipleInputFeatureRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.StepInputExpressionRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.LoadListingRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.InplaceUpdateRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.SecretsLoader: Final

cwl_utils.parser.cwl_v1_0.TimeLimitLoader: Final

cwl_utils.parser.cwl_v1_0.WorkReuseLoader: Final

cwl_utils.parser.cwl_v1_0.NetworkAccessLoader: Final

cwl_utils.parser.cwl_v1_0.ProcessGeneratorLoader: Final

cwl_utils.parser.cwl_v1_0.MPIRequirementLoader: Final

cwl_utils.parser.cwl_v1_0.CUDARequirementLoader: Final

cwl_utils.parser.cwl_v1_0.ShmSizeLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_strtype: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_strtype_or_array_of_strtype: Final

cwl_utils.parser.cwl_v1_0.uri_strtype_True_False_None_None: Final

cwl_utils.parser.cwl_v1_0.union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.typedsl_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype_2: Final

cwl_utils.parser.cwl_v1_0.array_of_RecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_array_of_RecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_fields_union_of_None_type_or_array_of_RecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.Record_nameLoader: Final

cwl_utils.parser.cwl_v1_0.typedsl_Record_nameLoader_2: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_strtype: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_None_type_or_strtype_True_False_None_None: Final

cwl_utils.parser.cwl_v1_0.uri_array_of_strtype_True_False_None_None: Final

cwl_utils.parser.cwl_v1_0.Enum_nameLoader: Final

cwl_utils.parser.cwl_v1_0.typedsl_Enum_nameLoader_2: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_MapSchemaLoader_or_UnionSchemaLoader_or_strtype_False_True_2_None: Final

cwl_utils.parser.cwl_v1_0.Array_nameLoader: Final

cwl_utils.parser.cwl_v1_0.typedsl_Array_nameLoader_2: Final

cwl_utils.parser.cwl_v1_0.Map_nameLoader: Final

cwl_utils.parser.cwl_v1_0.typedsl_Map_nameLoader_2: Final

cwl_utils.parser.cwl_v1_0.Union_nameLoader: Final

cwl_utils.parser.cwl_v1_0.typedsl_Union_nameLoader_2: Final

cwl_utils.parser.cwl_v1_0.union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.array_of_union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype_False_True_2_None: Final

cwl_utils.parser.cwl_v1_0.typedsl_union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_CWLRecordSchemaLoader_or_EnumSchemaLoader_or_CWLArraySchemaLoader_or_strtype_2: Final

cwl_utils.parser.cwl_v1_0.array_of_CWLRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_array_of_CWLRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_fields_union_of_None_type_or_array_of_CWLRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.File_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_File_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_None_type_or_strtype_False_False_None_None: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_inttype: Final

cwl_utils.parser.cwl_v1_0.union_of_FileLoader_or_DirectoryLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_union_of_FileLoader_or_DirectoryLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_array_of_union_of_FileLoader_or_DirectoryLoader: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_None_type_or_strtype_True_False_None_True: Final

cwl_utils.parser.cwl_v1_0.Directory_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_Directory_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.union_of_strtype_or_ExpressionLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_union_of_strtype_or_ExpressionLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_strtype_or_ExpressionLoader_or_array_of_union_of_strtype_or_ExpressionLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_booltype: Final

cwl_utils.parser.cwl_v1_0.union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.typedsl_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_2: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_InputBindingProxyLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_InputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_array_of_InputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_fields_union_of_None_type_or_array_of_InputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_False_True_2_None: Final

cwl_utils.parser.cwl_v1_0.union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.typedsl_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_2: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_OutputBindingProxyLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_OutputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_array_of_OutputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_fields_union_of_None_type_or_array_of_OutputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_False_True_2_None: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_strtype_or_array_of_strtype_or_ExpressionLoader: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_None_type_or_strtype_or_array_of_strtype_or_ExpressionLoader_True_False_None_True: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_InputParameterTypeLoader: Final

cwl_utils.parser.cwl_v1_0.typedsl_union_of_None_type_or_InputParameterTypeLoader_2: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_strtype_or_ExpressionLoader: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_None_type_or_strtype_or_ExpressionLoader_True_False_None_True: Final

cwl_utils.parser.cwl_v1_0.array_of_InputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_inputs_array_of_InputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_OutputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_outputs_array_of_OutputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_LoadListingRequirementLoader_or_EnvVarRequirementLoader_or_WorkReuseLoader_or_DockerRequirementLoader_or_SoftwareRequirementLoader_or_InitialWorkDirRequirementLoader_or_ScatterFeatureRequirementLoader_or_MPIRequirementLoader_or_SchemaDefRequirementLoader_or_InlineJavascriptRequirementLoader_or_InplaceUpdateRequirementLoader_or_CUDARequirementLoader_or_ResourceRequirementLoader_or_StepInputExpressionRequirementLoader_or_MultipleInputFeatureRequirementLoader_or_SubworkflowFeatureRequirementLoader_or_ShellCommandRequirementLoader_or_TimeLimitLoader_or_SecretsLoader_or_ShmSizeLoader_or_NetworkAccessLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_ProcessRequirementProxyLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_array_of_ProcessRequirementProxyLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_requirements_union_of_None_type_or_array_of_ProcessRequirementProxyLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_ProcessRequirementProxyLoader_or_Any_type: Final

cwl_utils.parser.cwl_v1_0.array_of_union_of_ProcessRequirementProxyLoader_or_Any_type: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_array_of_union_of_ProcessRequirementProxyLoader_or_Any_type: Final

cwl_utils.parser.cwl_v1_0.idmap_hints_union_of_None_type_or_array_of_union_of_ProcessRequirementProxyLoader_or_Any_type: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_CWLVersionLoader: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_None_type_or_CWLVersionLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.InlineJavascriptRequirement_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_InlineJavascriptRequirement_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_array_of_strtype: Final

cwl_utils.parser.cwl_v1_0.SchemaDefRequirement_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_SchemaDefRequirement_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.union_of_InputRecordSchemaLoader_or_InputArraySchemaLoader_or_InputEnumSchemaLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_InputSchemaProxyLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_strtype_or_ExpressionLoader_or_array_of_strtype: Final

cwl_utils.parser.cwl_v1_0.union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.typedsl_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_2: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_CommandLineBindingLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_CommandInputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_array_of_CommandInputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_fields_union_of_None_type_or_array_of_CommandInputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_False_True_2_None: Final

cwl_utils.parser.cwl_v1_0.union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype: Final

cwl_utils.parser.cwl_v1_0.typedsl_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_2: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_CommandOutputBindingLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_CommandOutputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_array_of_CommandOutputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_fields_union_of_None_type_or_array_of_CommandOutputRecordFieldLoader: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_False_True_2_None: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_CommandInputParameterTypeLoader: Final

cwl_utils.parser.cwl_v1_0.typedsl_union_of_None_type_or_CommandInputParameterTypeLoader_2: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_CommandOutputParameterTypeLoader: Final

cwl_utils.parser.cwl_v1_0.typedsl_union_of_None_type_or_CommandOutputParameterTypeLoader_2: Final

cwl_utils.parser.cwl_v1_0.CommandLineTool_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_CommandLineTool_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.array_of_CommandInputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_inputs_array_of_CommandInputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_CommandOutputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_outputs_array_of_CommandOutputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_strtype_or_ExpressionLoader_or_CommandLineBindingLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_union_of_strtype_or_ExpressionLoader_or_CommandLineBindingLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_array_of_union_of_strtype_or_ExpressionLoader_or_CommandLineBindingLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_inttype: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_array_of_inttype: Final

cwl_utils.parser.cwl_v1_0.DockerRequirement_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_DockerRequirement_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.SoftwareRequirement_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_SoftwareRequirement_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.array_of_SoftwarePackageLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_packages_array_of_SoftwarePackageLoader: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_None_type_or_array_of_strtype_False_False_None_True: Final

cwl_utils.parser.cwl_v1_0.InitialWorkDirRequirement_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_InitialWorkDirRequirement_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.union_of_FileLoader_or_DirectoryLoader_or_DirentLoader_or_strtype_or_ExpressionLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_union_of_FileLoader_or_DirectoryLoader_or_DirentLoader_or_strtype_or_ExpressionLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_array_of_union_of_FileLoader_or_DirectoryLoader_or_DirentLoader_or_strtype_or_ExpressionLoader_or_strtype_or_ExpressionLoader: Final

cwl_utils.parser.cwl_v1_0.EnvVarRequirement_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_EnvVarRequirement_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.array_of_EnvironmentDefLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_envDef_array_of_EnvironmentDefLoader: Final

cwl_utils.parser.cwl_v1_0.ShellCommandRequirement_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_ShellCommandRequirement_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.ResourceRequirement_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_ResourceRequirement_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_inttype_or_strtype_or_ExpressionLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_OutputParameterTypeLoader: Final

cwl_utils.parser.cwl_v1_0.typedsl_union_of_None_type_or_OutputParameterTypeLoader_2: Final

cwl_utils.parser.cwl_v1_0.ExpressionTool_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_ExpressionTool_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.array_of_ExpressionToolOutputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_outputs_array_of_ExpressionToolOutputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_None_type_or_strtype_or_array_of_strtype_False_False_1_None: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_LinkMergeMethodLoader: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_None_type_or_strtype_or_array_of_strtype_False_False_2_None: Final

cwl_utils.parser.cwl_v1_0.array_of_WorkflowStepInputLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_in__array_of_WorkflowStepInputLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_strtype_or_WorkflowStepOutputLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_union_of_strtype_or_WorkflowStepOutputLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_array_of_union_of_strtype_or_WorkflowStepOutputLoader: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_array_of_union_of_strtype_or_WorkflowStepOutputLoader_True_False_None_None: Final

cwl_utils.parser.cwl_v1_0.array_of_Any_type: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_array_of_Any_type: Final

cwl_utils.parser.cwl_v1_0.idmap_hints_union_of_None_type_or_array_of_Any_type: Final

cwl_utils.parser.cwl_v1_0.union_of_ExpressionToolLoader_or_WorkflowLoader_or_ProcessGeneratorLoader_or_CommandLineToolLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_strtype_or_ProcessProxyLoader: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_strtype_or_ProcessProxyLoader_False_False_None_None: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_None_type_or_strtype_or_array_of_strtype_False_False_0_None: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_ScatterMethodLoader: Final

cwl_utils.parser.cwl_v1_0.uri_union_of_None_type_or_ScatterMethodLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.Workflow_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_Workflow_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.array_of_WorkflowOutputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_outputs_array_of_WorkflowOutputParameterLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_WorkflowStepLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_array_of_WorkflowStepLoader: Final

cwl_utils.parser.cwl_v1_0.idmap_steps_union_of_array_of_WorkflowStepLoader: Final

cwl_utils.parser.cwl_v1_0.SubworkflowFeatureRequirement_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_SubworkflowFeatureRequirement_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.ScatterFeatureRequirement_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_ScatterFeatureRequirement_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.MultipleInputFeatureRequirement_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_MultipleInputFeatureRequirement_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.StepInputExpressionRequirement_classLoader: Final

cwl_utils.parser.cwl_v1_0.uri_StepInputExpressionRequirement_classLoader_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.uri_strtype_False_True_None_None: Final

cwl_utils.parser.cwl_v1_0.LoadListingEnumLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_LoadListingEnumLoader: Final

cwl_utils.parser.cwl_v1_0.uri_array_of_strtype_False_False_0_None: Final

cwl_utils.parser.cwl_v1_0.union_of_inttype_or_strtype: Final

cwl_utils.parser.cwl_v1_0.union_of_booltype_or_strtype: Final

cwl_utils.parser.cwl_v1_0.union_of_inttype_or_ExpressionLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_strtype_or_array_of_strtype: Final

cwl_utils.parser.cwl_v1_0.union_of_None_type_or_inttype_or_ExpressionLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_CommandLineToolLoader_or_ExpressionToolLoader_or_WorkflowLoader_or_ProcessGeneratorLoader: Final

cwl_utils.parser.cwl_v1_0.array_of_union_of_CommandLineToolLoader_or_ExpressionToolLoader_or_WorkflowLoader_or_ProcessGeneratorLoader: Final

cwl_utils.parser.cwl_v1_0.union_of_CommandLineToolLoader_or_ExpressionToolLoader_or_WorkflowLoader_or_ProcessGeneratorLoader_or_array_of_union_of_CommandLineToolLoader_or_ExpressionToolLoader_or_WorkflowLoader_or_ProcessGeneratorLoader: Final

cwl_utils.parser.cwl_v1_0.load_document(doc, baseuri=None, loadingOptions=None)

Parameters:

doc (Any)
baseuri (str | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

Return type:

Any

cwl_utils.parser.cwl_v1_0.load_document_with_metadata(doc, baseuri=None, loadingOptions=None, addl_metadata_fields=None)

Parameters:

doc (Any)
baseuri (str | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)
addl_metadata_fields (collections.abc.MutableSequence[str] | None)

Return type:

Any

cwl_utils.parser.cwl_v1_0.load_document_by_string(string, uri, loadingOptions=None)

Parameters:

string (Any)
uri (str)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

Return type:

Any

cwl_utils.parser.cwl_v1_0.load_document_by_yaml(yaml, uri, loadingOptions=None)

Shortcut to load via a YAML object. yaml: must be from ruamel.yaml.main.YAML.load with preserve_quotes=True

Parameters:

yaml (Any)
uri (str)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

Return type:

Any