cwl_utils.parser.cwl_v1_1

Attributes

`IdxType`
`save_type`
`strtype`
`inttype`
`floattype`
`booltype`
`None_type`
`Any_type`
`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`
`InlineJavascriptRequirementLoader`
`SchemaDefRequirementLoader`
`LoadListingRequirementLoader`
`DockerRequirementLoader`
`SoftwareRequirementLoader`
`InitialWorkDirRequirementLoader`
`EnvVarRequirementLoader`
`ShellCommandRequirementLoader`
`ResourceRequirementLoader`
`WorkReuseLoader`
`NetworkAccessLoader`
`InplaceUpdateRequirementLoader`
`ToolTimeLimitLoader`
`SubworkflowFeatureRequirementLoader`
`ScatterFeatureRequirementLoader`
`MultipleInputFeatureRequirementLoader`
`StepInputExpressionRequirementLoader`
`SecretsLoader`
`MPIRequirementLoader`
`CUDARequirementLoader`
`ShmSizeLoader`
union_of_InlineJavascriptRequirementLoader_or_SchemaDefRequirementLoader_or_LoadListingRequirementLoader_or_DockerRequirementLoader_or_SoftwareRequirementLoader_or_InitialWorkDirRequirementLoader_or_EnvVarRequirementLoader_or_ShellCommandRequirementLoader_or_ResourceRequirementLoader_or_WorkReuseLoader_or_NetworkAccessLoader_or_InplaceUpdateRequirementLoader_or_ToolTimeLimitLoader_or_SubworkflowFeatureRequirementLoader_or_ScatterFeatureRequirementLoader_or_MultipleInputFeatureRequirementLoader_or_StepInputExpressionRequirementLoader_or_SecretsLoader_or_MPIRequirementLoader_or_CUDARequirementLoader_or_ShmSizeLoader
array_of_union_of_InlineJavascriptRequirementLoader_or_SchemaDefRequirementLoader_or_LoadListingRequirementLoader_or_DockerRequirementLoader_or_SoftwareRequirementLoader_or_InitialWorkDirRequirementLoader_or_EnvVarRequirementLoader_or_ShellCommandRequirementLoader_or_ResourceRequirementLoader_or_WorkReuseLoader_or_NetworkAccessLoader_or_InplaceUpdateRequirementLoader_or_ToolTimeLimitLoader_or_SubworkflowFeatureRequirementLoader_or_ScatterFeatureRequirementLoader_or_MultipleInputFeatureRequirementLoader_or_StepInputExpressionRequirementLoader_or_SecretsLoader_or_MPIRequirementLoader_or_CUDARequirementLoader_or_ShmSizeLoader
union_of_None_type_or_array_of_union_of_InlineJavascriptRequirementLoader_or_SchemaDefRequirementLoader_or_LoadListingRequirementLoader_or_DockerRequirementLoader_or_SoftwareRequirementLoader_or_InitialWorkDirRequirementLoader_or_EnvVarRequirementLoader_or_ShellCommandRequirementLoader_or_ResourceRequirementLoader_or_WorkReuseLoader_or_NetworkAccessLoader_or_InplaceUpdateRequirementLoader_or_ToolTimeLimitLoader_or_SubworkflowFeatureRequirementLoader_or_ScatterFeatureRequirementLoader_or_MultipleInputFeatureRequirementLoader_or_StepInputExpressionRequirementLoader_or_SecretsLoader_or_MPIRequirementLoader_or_CUDARequirementLoader_or_ShmSizeLoader_or_CWLObjectTypeLoader
map_of_union_of_None_type_or_array_of_union_of_InlineJavascriptRequirementLoader_or_SchemaDefRequirementLoader_or_LoadListingRequirementLoader_or_DockerRequirementLoader_or_SoftwareRequirementLoader_or_InitialWorkDirRequirementLoader_or_EnvVarRequirementLoader_or_ShellCommandRequirementLoader_or_ResourceRequirementLoader_or_WorkReuseLoader_or_NetworkAccessLoader_or_InplaceUpdateRequirementLoader_or_ToolTimeLimitLoader_or_SubworkflowFeatureRequirementLoader_or_ScatterFeatureRequirementLoader_or_MultipleInputFeatureRequirementLoader_or_StepInputExpressionRequirementLoader_or_SecretsLoader_or_MPIRequirementLoader_or_CUDARequirementLoader_or_ShmSizeLoader_or_CWLObjectTypeLoader
`CWLInputFileLoader`
`CWLVersionLoader`	Version symbols for published CWL document versions.
`LoadListingEnumLoader`	Specify the desired behavior for loading the listing field of
`ExpressionLoader`
`InputBindingLoader`
`InputRecordFieldLoader`
`InputRecordSchemaLoader`
`InputEnumSchemaLoader`
`InputArraySchemaLoader`
`OutputRecordFieldLoader`
`OutputRecordSchemaLoader`
`OutputEnumSchemaLoader`
`OutputArraySchemaLoader`
`SecondaryFileSchemaLoader`
`EnvironmentDefLoader`
`CommandLineBindingLoader`
`CommandOutputBindingLoader`
`CommandLineBindableLoader`
`CommandInputRecordFieldLoader`
`CommandInputRecordSchemaLoader`
`CommandInputEnumSchemaLoader`
`CommandInputArraySchemaLoader`
`CommandOutputRecordFieldLoader`
`CommandOutputRecordSchemaLoader`
`CommandOutputEnumSchemaLoader`
`CommandOutputArraySchemaLoader`
`CommandInputParameterLoader`
`CommandOutputParameterLoader`
`stdinLoader`	Only valid as a type for a CommandLineTool input with no
`stdoutLoader`	Only valid as a type for a CommandLineTool output with no
`stderrLoader`	Only valid as a type for a CommandLineTool output with no
`CommandLineToolLoader`
`SoftwarePackageLoader`
`DirentLoader`
`ExpressionToolOutputParameterLoader`
`WorkflowInputParameterLoader`
`ExpressionToolLoader`
`LinkMergeMethodLoader`	The input link merge method, described in [WorkflowStepInput](#WorkflowStepInput).
`WorkflowOutputParameterLoader`
`WorkflowStepInputLoader`
`WorkflowStepOutputLoader`
`ScatterMethodLoader`	The scatter method, as described in [workflow step scatter](#WorkflowStep).
`WorkflowStepLoader`
`WorkflowLoader`
`ProcessGeneratorLoader`
`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`
`secondaryfilesdsl_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_None_type_or_booltype`
`union_of_None_type_or_LoadListingEnumLoader`
`array_of_SecondaryFileSchemaLoader`
`union_of_None_type_or_SecondaryFileSchemaLoader_or_array_of_SecondaryFileSchemaLoader`
`secondaryfilesdsl_union_of_None_type_or_SecondaryFileSchemaLoader_or_array_of_SecondaryFileSchemaLoader`
`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_strtype_or_ExpressionLoader`
`uri_union_of_None_type_or_strtype_or_ExpressionLoader_True_False_None_True`
`union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype`
`array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype`
`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`
`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`
`array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype`
`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`
`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_CommandInputParameterLoader_or_WorkflowInputParameterLoader`
`array_of_union_of_CommandInputParameterLoader_or_WorkflowInputParameterLoader`
`idmap_inputs_array_of_union_of_CommandInputParameterLoader_or_WorkflowInputParameterLoader`
`union_of_CommandOutputParameterLoader_or_ExpressionToolOutputParameterLoader_or_WorkflowOutputParameterLoader`
`array_of_union_of_CommandOutputParameterLoader_or_ExpressionToolOutputParameterLoader_or_WorkflowOutputParameterLoader`
`idmap_outputs_array_of_union_of_CommandOutputParameterLoader_or_ExpressionToolOutputParameterLoader_or_WorkflowOutputParameterLoader`
union_of_None_type_or_array_of_union_of_InlineJavascriptRequirementLoader_or_SchemaDefRequirementLoader_or_LoadListingRequirementLoader_or_DockerRequirementLoader_or_SoftwareRequirementLoader_or_InitialWorkDirRequirementLoader_or_EnvVarRequirementLoader_or_ShellCommandRequirementLoader_or_ResourceRequirementLoader_or_WorkReuseLoader_or_NetworkAccessLoader_or_InplaceUpdateRequirementLoader_or_ToolTimeLimitLoader_or_SubworkflowFeatureRequirementLoader_or_ScatterFeatureRequirementLoader_or_MultipleInputFeatureRequirementLoader_or_StepInputExpressionRequirementLoader_or_SecretsLoader_or_MPIRequirementLoader_or_CUDARequirementLoader_or_ShmSizeLoader
idmap_requirements_union_of_None_type_or_array_of_union_of_InlineJavascriptRequirementLoader_or_SchemaDefRequirementLoader_or_LoadListingRequirementLoader_or_DockerRequirementLoader_or_SoftwareRequirementLoader_or_InitialWorkDirRequirementLoader_or_EnvVarRequirementLoader_or_ShellCommandRequirementLoader_or_ResourceRequirementLoader_or_WorkReuseLoader_or_NetworkAccessLoader_or_InplaceUpdateRequirementLoader_or_ToolTimeLimitLoader_or_SubworkflowFeatureRequirementLoader_or_ScatterFeatureRequirementLoader_or_MultipleInputFeatureRequirementLoader_or_StepInputExpressionRequirementLoader_or_SecretsLoader_or_MPIRequirementLoader_or_CUDARequirementLoader_or_ShmSizeLoader
union_of_InlineJavascriptRequirementLoader_or_SchemaDefRequirementLoader_or_LoadListingRequirementLoader_or_DockerRequirementLoader_or_SoftwareRequirementLoader_or_InitialWorkDirRequirementLoader_or_EnvVarRequirementLoader_or_ShellCommandRequirementLoader_or_ResourceRequirementLoader_or_WorkReuseLoader_or_NetworkAccessLoader_or_InplaceUpdateRequirementLoader_or_ToolTimeLimitLoader_or_SubworkflowFeatureRequirementLoader_or_ScatterFeatureRequirementLoader_or_MultipleInputFeatureRequirementLoader_or_StepInputExpressionRequirementLoader_or_SecretsLoader_or_MPIRequirementLoader_or_CUDARequirementLoader_or_ShmSizeLoader_or_Any_type
array_of_union_of_InlineJavascriptRequirementLoader_or_SchemaDefRequirementLoader_or_LoadListingRequirementLoader_or_DockerRequirementLoader_or_SoftwareRequirementLoader_or_InitialWorkDirRequirementLoader_or_EnvVarRequirementLoader_or_ShellCommandRequirementLoader_or_ResourceRequirementLoader_or_WorkReuseLoader_or_NetworkAccessLoader_or_InplaceUpdateRequirementLoader_or_ToolTimeLimitLoader_or_SubworkflowFeatureRequirementLoader_or_ScatterFeatureRequirementLoader_or_MultipleInputFeatureRequirementLoader_or_StepInputExpressionRequirementLoader_or_SecretsLoader_or_MPIRequirementLoader_or_CUDARequirementLoader_or_ShmSizeLoader_or_Any_type
union_of_None_type_or_array_of_union_of_InlineJavascriptRequirementLoader_or_SchemaDefRequirementLoader_or_LoadListingRequirementLoader_or_DockerRequirementLoader_or_SoftwareRequirementLoader_or_InitialWorkDirRequirementLoader_or_EnvVarRequirementLoader_or_ShellCommandRequirementLoader_or_ResourceRequirementLoader_or_WorkReuseLoader_or_NetworkAccessLoader_or_InplaceUpdateRequirementLoader_or_ToolTimeLimitLoader_or_SubworkflowFeatureRequirementLoader_or_ScatterFeatureRequirementLoader_or_MultipleInputFeatureRequirementLoader_or_StepInputExpressionRequirementLoader_or_SecretsLoader_or_MPIRequirementLoader_or_CUDARequirementLoader_or_ShmSizeLoader_or_Any_type
idmap_hints_union_of_None_type_or_array_of_union_of_InlineJavascriptRequirementLoader_or_SchemaDefRequirementLoader_or_LoadListingRequirementLoader_or_DockerRequirementLoader_or_SoftwareRequirementLoader_or_InitialWorkDirRequirementLoader_or_EnvVarRequirementLoader_or_ShellCommandRequirementLoader_or_ResourceRequirementLoader_or_WorkReuseLoader_or_NetworkAccessLoader_or_InplaceUpdateRequirementLoader_or_ToolTimeLimitLoader_or_SubworkflowFeatureRequirementLoader_or_ScatterFeatureRequirementLoader_or_MultipleInputFeatureRequirementLoader_or_StepInputExpressionRequirementLoader_or_SecretsLoader_or_MPIRequirementLoader_or_CUDARequirementLoader_or_ShmSizeLoader_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_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader`
`array_of_union_of_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader`
`union_of_strtype_or_ExpressionLoader`
`union_of_None_type_or_booltype_or_ExpressionLoader`
`LoadListingRequirement_classLoader`
`uri_LoadListingRequirement_classLoader_False_True_None_None`
`union_of_None_type_or_inttype_or_ExpressionLoader`
`union_of_None_type_or_strtype_or_ExpressionLoader_or_array_of_strtype`
`union_of_None_type_or_ExpressionLoader`
`union_of_None_type_or_CommandLineBindingLoader`
`union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype`
`array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_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`
`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`
`array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype`
`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_CWLTypeLoader_or_stdinLoader_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_stdinLoader_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_CWLTypeLoader_or_stdoutLoader_or_stderrLoader_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_stdoutLoader_or_stderrLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_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_None_type_or_FileLoader_or_array_of_union_of_FileLoader_or_DirectoryLoader_or_DirectoryLoader_or_DirentLoader_or_ExpressionLoader`
`array_of_union_of_None_type_or_FileLoader_or_array_of_union_of_FileLoader_or_DirectoryLoader_or_DirectoryLoader_or_DirentLoader_or_ExpressionLoader`
`union_of_array_of_union_of_None_type_or_FileLoader_or_array_of_union_of_FileLoader_or_DirectoryLoader_or_DirectoryLoader_or_DirentLoader_or_ExpressionLoader_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`
`WorkReuse_classLoader`
`uri_WorkReuse_classLoader_False_True_None_None`
`union_of_booltype_or_ExpressionLoader`
`NetworkAccess_classLoader`
`uri_NetworkAccess_classLoader_False_True_None_None`
`InplaceUpdateRequirement_classLoader`
`uri_InplaceUpdateRequirement_classLoader_False_True_None_None`
`ToolTimeLimit_classLoader`
`uri_ToolTimeLimit_classLoader_False_True_None_None`
`union_of_inttype_or_ExpressionLoader`
`union_of_None_type_or_InputBindingLoader`
`ExpressionTool_classLoader`
`uri_ExpressionTool_classLoader_False_True_None_None`
`array_of_WorkflowInputParameterLoader`
`idmap_inputs_array_of_WorkflowInputParameterLoader`
`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_strtype_or_CommandLineToolLoader_or_ExpressionToolLoader_or_WorkflowLoader_or_ProcessGeneratorLoader`
`uri_union_of_strtype_or_CommandLineToolLoader_or_ExpressionToolLoader_or_WorkflowLoader_or_ProcessGeneratorLoader_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`
`uri_array_of_strtype_False_False_0_None`
`union_of_strtype_or_array_of_strtype`
`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

`LoadingOptions`
`Saveable`	Mark classes than have a save() and fromDoc() function.
`Documented`	Mark classes than have a save() and fromDoc() function.
`RecordField`	A field of a record.
`RecordSchema`	Mark classes than have a save() and fromDoc() function.
`EnumSchema`	Define an enumerated type.
`ArraySchema`	Mark classes than have a save() and fromDoc() function.
`MapSchema`	Mark classes than have a save() and fromDoc() function.
`UnionSchema`	Mark classes than have a save() and fromDoc() function.
`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
`Directory`	Represents a directory to present to a command line tool.
`Labeled`	Mark classes than have a save() and fromDoc() function.
`Identified`	Mark classes than have a save() and fromDoc() function.
`LoadContents`	Mark classes than have a save() and fromDoc() function.
`FieldBase`	Mark classes than have a save() and fromDoc() function.
`InputFormat`	Mark classes than have a save() and fromDoc() function.
`OutputFormat`	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.
`IOSchema`	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
`Process`	The base executable type in CWL is the Process object defined by the
`InlineJavascriptRequirement`	Indicates that the workflow platform must support inline Javascript expressions.
`CommandInputSchema`	Mark classes than have a save() and fromDoc() function.
`SchemaDefRequirement`	This field consists of an array of type definitions which must be used when
`SecondaryFileSchema`	Mark classes than have a save() and fromDoc() function.
`LoadListingRequirement`	Specify the desired behavior for loading the listing field of
`EnvironmentDef`	Define an environment variable that will be set in the runtime environment
`CommandLineBinding`	When listed under inputBinding in the input schema, the term
`CommandOutputBinding`	Describes how to generate an output parameter based on the files produced
`CommandLineBindable`	Mark classes than have a save() and fromDoc() function.
`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
`SoftwareRequirement`	A list of software packages that should be configured in the environment of
`SoftwarePackage`	Mark classes than have a save() and fromDoc() function.
`Dirent`	Define a file or subdirectory that must be placed in the designated output
`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
`ShellCommandRequirement`	Modify the behavior of CommandLineTool to generate a single string
`ResourceRequirement`	Specify basic hardware resource requirements.
`WorkReuse`	For implementations that support reusing output from past work (on
`NetworkAccess`	Indicate whether a process requires outgoing IPv4/IPv6 network
`InplaceUpdateRequirement`	If inplaceUpdate is true, then an implementation supporting this
`ToolTimeLimit`	Set an upper limit on the execution time of a CommandLineTool.
`ExpressionToolOutputParameter`	Define an input or output parameter to a process.
`WorkflowInputParameter`	Define an input or output parameter to a process.
`ExpressionTool`	An ExpressionTool is a type of Process object that can be run by itself
`WorkflowOutputParameter`	Describe an output parameter of a workflow. The parameter must be
`Sink`	Mark classes than have a save() and fromDoc() function.
`WorkflowStepInput`	The input of a workflow step connects an upstream parameter (from the
`WorkflowStepOutput`	Associate an output parameter of the underlying process with a workflow
`WorkflowStep`	A workflow step is an executable element of a workflow. It specifies the
`Workflow`	A workflow describes a set of steps and the dependencies between
`SubworkflowFeatureRequirement`	Indicates that the workflow platform must support nested workflows in
`ScatterFeatureRequirement`	Indicates that the workflow platform must support the scatter and
`MultipleInputFeatureRequirement`	Indicates that the workflow platform must support multiple inbound data links
`StepInputExpressionRequirement`	Indicate that the workflow platform must support the valueFrom field
`Secrets`	A process requirement declares a prerequisite that may or must be fulfilled
`ProcessGenerator`	The base executable type in CWL is the Process object defined by the
`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

Functions

`load_field`(val, fieldtype, baseuri, loadingOptions[, lc])	Load field.
`extract_type`(val_type)	Take a type of value, and extracts the value as a string.
`convert_typing`(val_type)	Normalize type names to schema-salad types.
`parse_errors`(error_message)	Parse error messages from several loaders into one error message.
`save`(val[, top, base_url, relative_uris])
`save_with_metadata`(val, valLoadingOpts[, top, ...])	Save and set $namespaces, $schemas, $base and any other metadata fields at the top level.
`expand_url`(url, base_url, loadingOptions[, scoped_id, ...])
`file_uri`(path[, split_frag])	Transform a file path into a URL with file scheme.
`prefix_url`(url, namespaces)	Expand short forms into full URLs using the given namespace dictionary.
`save_relative_uri`(uri, base_url, scoped_id, ref_scope, ...)	Convert any URI to a relative one, obeying the scoping rules.
`shortname`(inputid)	Compute the shortname of a fully qualified identifier.
`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_1.IdxType

class cwl_utils.parser.cwl_v1_1.LoadingOptions(fetcher=None, namespaces=None, schemas=None, fileuri=None, copyfrom=None, original_doc=None, addl_metadata=None, baseuri=None, idx=None, imports=None, includes=None, no_link_check=None, container=None)

Parameters:

fetcher (Optional[schema_salad.fetcher.Fetcher])
namespaces (Optional[dict[str, str]])
schemas (Optional[list[str]])
fileuri (Optional[str])
copyfrom (Optional[LoadingOptions])
original_doc (Optional[Any])
addl_metadata (Optional[dict[str, str]])
baseuri (Optional[str])
idx (Optional[IdxType])
imports (Optional[list[str]])
includes (Optional[list[str]])
no_link_check (Optional[bool])
container (Optional[str])

idx: IdxType

fileuri: str | None

baseuri: str

namespaces: collections.abc.MutableMapping[str, str]

schemas: collections.abc.MutableSequence[str]

original_doc: Any | None

addl_metadata: collections.abc.MutableMapping[str, Any]

fetcher: schema_salad.fetcher.Fetcher

vocab: dict[str, str]

rvocab: dict[str, str]

cache: schema_salad.utils.CacheType

imports: list[str]

includes: list[str]

no_link_check: bool | None

container: str | None

property graph: rdflib.Graph

Generate a merged rdflib.Graph from all entries in self.schemas.

Return type:: rdflib.Graph

class cwl_utils.parser.cwl_v1_1.Saveable

Bases: abc.ABC

Inheritance diagram of cwl_utils.parser.cwl_v1_1.Saveable

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

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

Abstractmethod:

Parameters:

_doc (Any)
baseuri (str)
loadingOptions (LoadingOptions)
docRoot (Optional[str])

Return type:

Saveable

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

abstract 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]

cwl_utils.parser.cwl_v1_1.load_field(val, fieldtype, baseuri, loadingOptions, lc=None)

Load field.

Parameters:

val (Union[str, dict[str, str]])
fieldtype (_Loader)
baseuri (str)
loadingOptions (LoadingOptions)
lc (Optional[list[Any]])

Return type:

Any

cwl_utils.parser.cwl_v1_1.save_type

cwl_utils.parser.cwl_v1_1.extract_type(val_type)

Take a type of value, and extracts the value as a string.

Parameters:: val_type (type[Any])
Return type:: str

cwl_utils.parser.cwl_v1_1.convert_typing(val_type)

Normalize type names to schema-salad types.

Parameters:: val_type (str)
Return type:: str

cwl_utils.parser.cwl_v1_1.parse_errors(error_message)

Parse error messages from several loaders into one error message.

Parameters:: error_message (str)
Return type:: tuple[str, str, str]

cwl_utils.parser.cwl_v1_1.save(val, top=True, base_url='', relative_uris=True)

Parameters:

val (Any)
top (bool)
base_url (str)
relative_uris (bool)

Return type:

save_type

cwl_utils.parser.cwl_v1_1.save_with_metadata(val, valLoadingOpts, top=True, base_url='', relative_uris=True)

Save and set $namespaces, $schemas, $base and any other metadata fields at the top level.

Parameters:

val (Any)
valLoadingOpts (LoadingOptions)
top (bool)
base_url (str)
relative_uris (bool)

Return type:

save_type

cwl_utils.parser.cwl_v1_1.expand_url(url, base_url, loadingOptions, scoped_id=False, vocab_term=False, scoped_ref=None)

Parameters:

url (str)
base_url (str)
loadingOptions (LoadingOptions)
scoped_id (bool)
vocab_term (bool)
scoped_ref (Optional[int])

Return type:

str

cwl_utils.parser.cwl_v1_1.file_uri(path, split_frag=False)

Transform a file path into a URL with file scheme.

Parameters:

path (str)
split_frag (bool)

Return type:

str

cwl_utils.parser.cwl_v1_1.prefix_url(url, namespaces)

Expand short forms into full URLs using the given namespace dictionary.

Parameters:

url (str)
namespaces (dict[str, str])

Return type:

str

cwl_utils.parser.cwl_v1_1.save_relative_uri(uri, base_url, scoped_id, ref_scope, relative_uris)

Convert any URI to a relative one, obeying the scoping rules.

Parameters:

uri (Any)
base_url (str)
scoped_id (bool)
ref_scope (Optional[int])
relative_uris (bool)

Return type:

Any

cwl_utils.parser.cwl_v1_1.shortname(inputid)

Compute the shortname of a fully qualified identifier.

See https://w3id.org/cwl/v1.2/SchemaSalad.html#Short_names.

Parameters:: inputid (str)
Return type:: str

cwl_utils.parser.cwl_v1_1.parser_info()

Return type:: str

class cwl_utils.parser.cwl_v1_1.Documented

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.Documented

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

class cwl_utils.parser.cwl_v1_1.RecordField(name, type_, doc=None, extension_fields=None, loadingOptions=None)

Bases: Documented

Inheritance diagram of cwl_utils.parser.cwl_v1_1.RecordField

A field of a record.

Parameters:

name (Any)
type_ (Any)
doc (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/salad#RecordField'

doc = None

name

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

RecordField

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

class cwl_utils.parser.cwl_v1_1.RecordSchema(type_, fields=None, extension_fields=None, loadingOptions=None)

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.RecordSchema

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

Parameters:

type_ (Any)
fields (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/salad#RecordSchema'

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

RecordSchema

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

class cwl_utils.parser.cwl_v1_1.EnumSchema(symbols, type_, name=None, extension_fields=None, loadingOptions=None)

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.EnumSchema

Define an enumerated type.

Parameters:

symbols (Any)
type_ (Any)
name (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/salad#EnumSchema'

name = None

symbols

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

EnumSchema

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

class cwl_utils.parser.cwl_v1_1.ArraySchema(items, type_, extension_fields=None, loadingOptions=None)

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.ArraySchema

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

Parameters:

items (Any)
type_ (Any)
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/salad#ArraySchema'

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

ArraySchema

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

class cwl_utils.parser.cwl_v1_1.MapSchema(type_, values, extension_fields=None, loadingOptions=None)

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.MapSchema

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

Parameters:

type_ (Any)
values (Any)
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/salad#MapSchema'

type_

values

__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 (LoadingOptions)
docRoot (Optional[str])

Return type:

MapSchema

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

class cwl_utils.parser.cwl_v1_1.UnionSchema(names, type_, extension_fields=None, loadingOptions=None)

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.UnionSchema

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

Parameters:

names (Any)
type_ (Any)
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/salad#UnionSchema'

names

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

UnionSchema

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

class cwl_utils.parser.cwl_v1_1.CWLArraySchema(items, type_, extension_fields=None, loadingOptions=None)

Bases: ArraySchema

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CWLArraySchema

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

Parameters:

items (Any)
type_ (Any)
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CWLArraySchema'

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CWLArraySchema

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

class cwl_utils.parser.cwl_v1_1.CWLRecordField(name, type_, doc=None, extension_fields=None, loadingOptions=None)

Bases: RecordField

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CWLRecordField

A field of a record.

Parameters:

name (Any)
type_ (Any)
doc (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CWLRecordField'

doc = None

name

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CWLRecordField

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

class cwl_utils.parser.cwl_v1_1.CWLRecordSchema(type_, fields=None, extension_fields=None, loadingOptions=None)

Bases: RecordSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CWLRecordSchema

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

Parameters:

type_ (Any)
fields (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CWLRecordSchema'

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CWLRecordSchema

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

class cwl_utils.parser.cwl_v1_1.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: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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 (Optional[Any])
path (Optional[Any])
basename (Optional[Any])
dirname (Optional[Any])
nameroot (Optional[Any])
nameext (Optional[Any])
checksum (Optional[Any])
size (Optional[Any])
secondaryFiles (Optional[Any])
format (Optional[Any])
contents (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#File'

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

File

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

class cwl_utils.parser.cwl_v1_1.Directory(location=None, path=None, basename=None, listing=None, extension_fields=None, loadingOptions=None)

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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 assigend.

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 (Optional[Any])
path (Optional[Any])
basename (Optional[Any])
listing (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#Directory'

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

Directory

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

class cwl_utils.parser.cwl_v1_1.Labeled

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.Labeled

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

class cwl_utils.parser.cwl_v1_1.Identified

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.Identified

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

class cwl_utils.parser.cwl_v1_1.LoadContents

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.LoadContents

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

class cwl_utils.parser.cwl_v1_1.FieldBase

Bases: Labeled

Inheritance diagram of cwl_utils.parser.cwl_v1_1.FieldBase

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

class cwl_utils.parser.cwl_v1_1.InputFormat

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.InputFormat

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

class cwl_utils.parser.cwl_v1_1.OutputFormat

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.OutputFormat

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

class cwl_utils.parser.cwl_v1_1.Parameter

Bases: FieldBase, Documented, Identified

Inheritance diagram of cwl_utils.parser.cwl_v1_1.Parameter

Define an input or output parameter to a process.

class cwl_utils.parser.cwl_v1_1.InputBinding(loadContents=None, extension_fields=None, loadingOptions=None)

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.InputBinding

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

Parameters:

loadContents (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#InputBinding'

loadContents = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

InputBinding

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

class cwl_utils.parser.cwl_v1_1.IOSchema

Bases: Labeled, Documented

Inheritance diagram of cwl_utils.parser.cwl_v1_1.IOSchema

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

class cwl_utils.parser.cwl_v1_1.InputSchema

Bases: IOSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_1.InputSchema

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

class cwl_utils.parser.cwl_v1_1.OutputSchema

Bases: IOSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_1.OutputSchema

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

class cwl_utils.parser.cwl_v1_1.InputRecordField(name, type_, doc=None, label=None, secondaryFiles=None, streamable=None, format=None, loadContents=None, loadListing=None, extension_fields=None, loadingOptions=None)

Bases: CWLRecordField, FieldBase, InputFormat, LoadContents

Inheritance diagram of cwl_utils.parser.cwl_v1_1.InputRecordField

A field of a record.

Parameters:

name (Any)
type_ (Any)
doc (Optional[Any])
label (Optional[Any])
secondaryFiles (Optional[Any])
streamable (Optional[Any])
format (Optional[Any])
loadContents (Optional[Any])
loadListing (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#InputRecordField'

doc = None

name

type_

label = None

secondaryFiles = None

streamable = None

format = None

loadContents = None

loadListing = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

InputRecordField

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

class cwl_utils.parser.cwl_v1_1.InputRecordSchema(type_, fields=None, label=None, doc=None, name=None, extension_fields=None, loadingOptions=None)

Bases: CWLRecordSchema, InputSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_1.InputRecordSchema

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

Parameters:

type_ (Any)
fields (Optional[Any])
label (Optional[Any])
doc (Optional[Any])
name (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#InputRecordSchema'

fields = None

type_

label = None

doc = None

name = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

InputRecordSchema

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

class cwl_utils.parser.cwl_v1_1.InputEnumSchema(symbols, type_, name=None, label=None, doc=None, extension_fields=None, loadingOptions=None)

Bases: EnumSchema, InputSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_1.InputEnumSchema

Define an enumerated type.

Parameters:

symbols (Any)
type_ (Any)
name (Optional[Any])
label (Optional[Any])
doc (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#InputEnumSchema'

name = None

symbols

type_

label = None

doc = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

InputEnumSchema

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

class cwl_utils.parser.cwl_v1_1.InputArraySchema(items, type_, label=None, doc=None, name=None, extension_fields=None, loadingOptions=None)

Bases: CWLArraySchema, InputSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_1.InputArraySchema

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

Parameters:

items (Any)
type_ (Any)
label (Optional[Any])
doc (Optional[Any])
name (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#InputArraySchema'

items

type_

label = None

doc = None

name = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

InputArraySchema

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

class cwl_utils.parser.cwl_v1_1.OutputRecordField(name, type_, doc=None, label=None, secondaryFiles=None, streamable=None, format=None, extension_fields=None, loadingOptions=None)

Bases: CWLRecordField, FieldBase, OutputFormat

Inheritance diagram of cwl_utils.parser.cwl_v1_1.OutputRecordField

A field of a record.

Parameters:

name (Any)
type_ (Any)
doc (Optional[Any])
label (Optional[Any])
secondaryFiles (Optional[Any])
streamable (Optional[Any])
format (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#OutputRecordField'

doc = None

name

type_

label = None

secondaryFiles = None

streamable = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

OutputRecordField

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

class cwl_utils.parser.cwl_v1_1.OutputRecordSchema(type_, fields=None, label=None, doc=None, name=None, extension_fields=None, loadingOptions=None)

Bases: CWLRecordSchema, OutputSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_1.OutputRecordSchema

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

Parameters:

type_ (Any)
fields (Optional[Any])
label (Optional[Any])
doc (Optional[Any])
name (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#OutputRecordSchema'

fields = None

type_

label = None

doc = None

name = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

OutputRecordSchema

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

class cwl_utils.parser.cwl_v1_1.OutputEnumSchema(symbols, type_, name=None, label=None, doc=None, extension_fields=None, loadingOptions=None)

Bases: EnumSchema, OutputSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_1.OutputEnumSchema

Define an enumerated type.

Parameters:

symbols (Any)
type_ (Any)
name (Optional[Any])
label (Optional[Any])
doc (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#OutputEnumSchema'

name = None

symbols

type_

label = None

doc = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

OutputEnumSchema

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

class cwl_utils.parser.cwl_v1_1.OutputArraySchema(items, type_, label=None, doc=None, name=None, extension_fields=None, loadingOptions=None)

Bases: CWLArraySchema, OutputSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_1.OutputArraySchema

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

Parameters:

items (Any)
type_ (Any)
label (Optional[Any])
doc (Optional[Any])
name (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#OutputArraySchema'

items

type_

label = None

doc = None

name = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

OutputArraySchema

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

class cwl_utils.parser.cwl_v1_1.InputParameter

Bases: Parameter, InputFormat, LoadContents

Inheritance diagram of cwl_utils.parser.cwl_v1_1.InputParameter

Define an input or output parameter to a process.

class cwl_utils.parser.cwl_v1_1.OutputParameter

Bases: Parameter, OutputFormat

Inheritance diagram of cwl_utils.parser.cwl_v1_1.OutputParameter

Define an input or output parameter to a process.

class cwl_utils.parser.cwl_v1_1.ProcessRequirement

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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_1.Process

Bases: Identified, Labeled, Documented

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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_1.InlineJavascriptRequirement(expressionLib=None, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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 (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#InlineJavascriptRequirement'

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

InlineJavascriptRequirement

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

class cwl_utils.parser.cwl_v1_1.CommandInputSchema

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CommandInputSchema

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

class cwl_utils.parser.cwl_v1_1.SchemaDefRequirement(types, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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 (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#SchemaDefRequirement'

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

SchemaDefRequirement

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

class cwl_utils.parser.cwl_v1_1.SecondaryFileSchema(pattern, required=None, extension_fields=None, loadingOptions=None)

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.SecondaryFileSchema

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

Parameters:

pattern (Any)
required (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#SecondaryFileSchema'

pattern

required = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

SecondaryFileSchema

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

class cwl_utils.parser.cwl_v1_1.LoadListingRequirement(loadListing=None, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_1.LoadListingRequirement

Specify the desired behavior for loading the listing field of a Directory object for use by expressions.

Parameters:

loadListing (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#LoadListingRequirement'

class_ = 'LoadListingRequirement'

loadListing = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

LoadListingRequirement

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

class cwl_utils.parser.cwl_v1_1.EnvironmentDef(envName, envValue, extension_fields=None, loadingOptions=None)

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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 (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#EnvironmentDef'

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

EnvironmentDef

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

class cwl_utils.parser.cwl_v1_1.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_1.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 (Optional[Any])
position (Optional[Any])
prefix (Optional[Any])
separate (Optional[Any])
itemSeparator (Optional[Any])
valueFrom (Optional[Any])
shellQuote (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CommandLineBinding'

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CommandLineBinding

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

class cwl_utils.parser.cwl_v1_1.CommandOutputBinding(loadContents=None, loadListing=None, glob=None, outputEval=None, extension_fields=None, loadingOptions=None)

Bases: LoadContents

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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:

loadContents (Optional[Any])
loadListing (Optional[Any])
glob (Optional[Any])
outputEval (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CommandOutputBinding'

loadContents = None

loadListing = None

glob = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CommandOutputBinding

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

class cwl_utils.parser.cwl_v1_1.CommandLineBindable(inputBinding=None, extension_fields=None, loadingOptions=None)

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CommandLineBindable

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

Parameters:

inputBinding (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CommandLineBindable'

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CommandLineBindable

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

class cwl_utils.parser.cwl_v1_1.CommandInputRecordField(name, type_, doc=None, label=None, secondaryFiles=None, streamable=None, format=None, loadContents=None, loadListing=None, inputBinding=None, extension_fields=None, loadingOptions=None)

Bases: InputRecordField, CommandLineBindable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CommandInputRecordField

A field of a record.

Parameters:

name (Any)
type_ (Any)
doc (Optional[Any])
label (Optional[Any])
secondaryFiles (Optional[Any])
streamable (Optional[Any])
format (Optional[Any])
loadContents (Optional[Any])
loadListing (Optional[Any])
inputBinding (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CommandInputRecordField'

doc = None

name

type_

label = None

secondaryFiles = None

streamable = None

format = None

loadContents = None

loadListing = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CommandInputRecordField

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

class cwl_utils.parser.cwl_v1_1.CommandInputRecordSchema(type_, fields=None, label=None, doc=None, name=None, inputBinding=None, extension_fields=None, loadingOptions=None)

Bases: InputRecordSchema, CommandInputSchema, CommandLineBindable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CommandInputRecordSchema

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

Parameters:

type_ (Any)
fields (Optional[Any])
label (Optional[Any])
doc (Optional[Any])
name (Optional[Any])
inputBinding (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CommandInputRecordSchema'

fields = None

type_

label = None

doc = None

name = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CommandInputRecordSchema

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

class cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema(symbols, type_, name=None, label=None, doc=None, inputBinding=None, extension_fields=None, loadingOptions=None)

Bases: InputEnumSchema, CommandInputSchema, CommandLineBindable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema

Define an enumerated type.

Parameters:

symbols (Any)
type_ (Any)
name (Optional[Any])
label (Optional[Any])
doc (Optional[Any])
inputBinding (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CommandInputEnumSchema'

name = None

symbols

type_

label = None

doc = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CommandInputEnumSchema

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

class cwl_utils.parser.cwl_v1_1.CommandInputArraySchema(items, type_, label=None, doc=None, name=None, inputBinding=None, extension_fields=None, loadingOptions=None)

Bases: InputArraySchema, CommandInputSchema, CommandLineBindable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CommandInputArraySchema

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

Parameters:

items (Any)
type_ (Any)
label (Optional[Any])
doc (Optional[Any])
name (Optional[Any])
inputBinding (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CommandInputArraySchema'

items

type_

label = None

doc = None

name = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CommandInputArraySchema

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

class cwl_utils.parser.cwl_v1_1.CommandOutputRecordField(name, type_, doc=None, label=None, secondaryFiles=None, streamable=None, format=None, outputBinding=None, extension_fields=None, loadingOptions=None)

Bases: OutputRecordField

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CommandOutputRecordField

A field of a record.

Parameters:

name (Any)
type_ (Any)
doc (Optional[Any])
label (Optional[Any])
secondaryFiles (Optional[Any])
streamable (Optional[Any])
format (Optional[Any])
outputBinding (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CommandOutputRecordField'

doc = None

name

type_

label = None

secondaryFiles = None

streamable = None

format = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CommandOutputRecordField

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

class cwl_utils.parser.cwl_v1_1.CommandOutputRecordSchema(type_, fields=None, label=None, doc=None, name=None, extension_fields=None, loadingOptions=None)

Bases: OutputRecordSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CommandOutputRecordSchema

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

Parameters:

type_ (Any)
fields (Optional[Any])
label (Optional[Any])
doc (Optional[Any])
name (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CommandOutputRecordSchema'

fields = None

type_

label = None

doc = None

name = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CommandOutputRecordSchema

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

class cwl_utils.parser.cwl_v1_1.CommandOutputEnumSchema(symbols, type_, name=None, label=None, doc=None, extension_fields=None, loadingOptions=None)

Bases: OutputEnumSchema

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CommandOutputEnumSchema

Define an enumerated type.

Parameters:

symbols (Any)
type_ (Any)
name (Optional[Any])
label (Optional[Any])
doc (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CommandOutputEnumSchema'

name = None

symbols

type_

label = None

doc = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CommandOutputEnumSchema

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

class cwl_utils.parser.cwl_v1_1.CommandOutputArraySchema(items, type_, label=None, doc=None, name=None, extension_fields=None, loadingOptions=None)

Bases: OutputArraySchema

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CommandOutputArraySchema

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

Parameters:

items (Any)
type_ (Any)
label (Optional[Any])
doc (Optional[Any])
name (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CommandOutputArraySchema'

items

type_

label = None

doc = None

name = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CommandOutputArraySchema

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

class cwl_utils.parser.cwl_v1_1.CommandInputParameter(type_, label=None, secondaryFiles=None, streamable=None, doc=None, id=None, format=None, loadContents=None, loadListing=None, default=None, inputBinding=None, extension_fields=None, loadingOptions=None)

Bases: InputParameter

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CommandInputParameter

An input parameter for a CommandLineTool.

Parameters:

type_ (Any)
label (Optional[Any])
secondaryFiles (Optional[Any])
streamable (Optional[Any])
doc (Optional[Any])
id (Optional[Any])
format (Optional[Any])
loadContents (Optional[Any])
loadListing (Optional[Any])
default (Optional[Any])
inputBinding (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CommandInputParameter'

label = None

secondaryFiles = None

streamable = None

doc = None

id = None

format = None

loadContents = None

loadListing = None

default = None

type_

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CommandInputParameter

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

class cwl_utils.parser.cwl_v1_1.CommandOutputParameter(type_, label=None, secondaryFiles=None, streamable=None, doc=None, id=None, format=None, outputBinding=None, extension_fields=None, loadingOptions=None)

Bases: OutputParameter

Inheritance diagram of cwl_utils.parser.cwl_v1_1.CommandOutputParameter

An output parameter for a CommandLineTool.

Parameters:

type_ (Any)
label (Optional[Any])
secondaryFiles (Optional[Any])
streamable (Optional[Any])
doc (Optional[Any])
id (Optional[Any])
format (Optional[Any])
outputBinding (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CommandOutputParameter'

label = None

secondaryFiles = None

streamable = None

doc = None

id = None

format = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CommandOutputParameter

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

class cwl_utils.parser.cwl_v1_1.CommandLineTool(inputs, outputs, id=None, label=None, doc=None, requirements=None, hints=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_1.CommandLineTool

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

Parameters:

inputs (Any)
outputs (Any)
id (Optional[Any])
label (Optional[Any])
doc (Optional[Any])
requirements (Optional[Any])
hints (Optional[Any])
cwlVersion (Optional[Any])
baseCommand (Optional[Any])
arguments (Optional[Any])
stdin (Optional[Any])
stderr (Optional[Any])
stdout (Optional[Any])
successCodes (Optional[Any])
temporaryFailCodes (Optional[Any])
permanentFailCodes (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#CommandLineTool'

id = None

label = None

doc = None

inputs

outputs

requirements = None

hints = None

cwlVersion = None

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

CommandLineTool

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

class cwl_utils.parser.cwl_v1_1.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_1.DockerRequirement

Indicates that a workflow component should be run in a [Docker](http://docker.com) or Docker-compatible (such as [Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment 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. The platform must ensure that runtime.outdir and runtime.tmpdir are distinct directories.

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.

A container image may specify an [ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint) and/or [CMD](https://docs.docker.com/engine/reference/builder/#cmd). Command line arguments will be appended after all elements of ENTRYPOINT, and will override all elements specified using CMD (in other words, CMD is only used when the CommandLineTool definition produces an empty command line).

Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility concerns of the implicit hidden execution point (For further discussion, see [https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD. CommandLineTools which do rely on ENTRYPOINT or CMD must list DockerRequirement in the requirements section.

## Interaction with other requirements

If [EnvVarRequirement](#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.

Parameters:

dockerPull (Optional[Any])
dockerLoad (Optional[Any])
dockerFile (Optional[Any])
dockerImport (Optional[Any])
dockerImageId (Optional[Any])
dockerOutputDirectory (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#DockerRequirement'

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

DockerRequirement

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

class cwl_utils.parser.cwl_v1_1.SoftwareRequirement(packages, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_1.SoftwareRequirement

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

Parameters:

packages (Any)
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#SoftwareRequirement'

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

SoftwareRequirement

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

class cwl_utils.parser.cwl_v1_1.SoftwarePackage(package, version=None, specs=None, extension_fields=None, loadingOptions=None)

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.SoftwarePackage

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

Parameters:

package (Any)
version (Optional[Any])
specs (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#SoftwarePackage'

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

SoftwarePackage

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

class cwl_utils.parser.cwl_v1_1.Dirent(entry, entryname=None, writable=None, extension_fields=None, loadingOptions=None)

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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 (Optional[Any])
writable (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#Dirent'

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

Dirent

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

class cwl_utils.parser.cwl_v1_1.InitialWorkDirRequirement(listing, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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 (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#InitialWorkDirRequirement'

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

InitialWorkDirRequirement

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

class cwl_utils.parser.cwl_v1_1.EnvVarRequirement(envDef, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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 (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#EnvVarRequirement'

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

EnvVarRequirement

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

class cwl_utils.parser.cwl_v1_1.ShellCommandRequirement(extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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 intepretation 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 (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#ShellCommandRequirement'

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

ShellCommandRequirement

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

class cwl_utils.parser.cwl_v1_1.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_1.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, use the default values below.

Parameters:

coresMin (Optional[Any])
coresMax (Optional[Any])
ramMin (Optional[Any])
ramMax (Optional[Any])
tmpdirMin (Optional[Any])
tmpdirMax (Optional[Any])
outdirMin (Optional[Any])
outdirMax (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#ResourceRequirement'

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

ResourceRequirement

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

class cwl_utils.parser.cwl_v1_1.WorkReuse(enableReuse, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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 accomodate 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 (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#WorkReuse'

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

WorkReuse

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

class cwl_utils.parser.cwl_v1_1.NetworkAccess(networkAccess, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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 publically routable IP address or the ability to accept inbound connections.

Parameters:

networkAccess (Any)
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#NetworkAccess'

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

NetworkAccess

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

class cwl_utils.parser.cwl_v1_1.InplaceUpdateRequirement(inplaceUpdate, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_1.InplaceUpdateRequirement

If inplaceUpdate is true, then an implementation supporting this feature may permit tools to directly update files with writable: true in InitialWorkDirRequirement. That is, as an optimization, files may be destructively modified in place as opposed to copied and updated.

An implementation must ensure that only one workflow step may access a writable file at a time. It is an error if a file which is writable by one workflow step file is accessed (for reading or writing) by any other workflow step running independently. However, a file which has been updated in a previous completed step may be used as input to multiple steps, provided it is read-only in every step.

Workflow steps which modify a file must produce the modified file as output. Downstream steps which futher process the file must use the output of previous steps, and not refer to a common input (this is necessary for both ordering and correctness).

Workflow authors should provide this in the hints section. The intent of this feature is that workflows produce the same results whether or not InplaceUpdateRequirement is supported by the implementation, and this feature is primarily available as an optimization for particular environments.

Users and implementers should be aware that workflows that destructively modify inputs may not be repeatable or reproducible. In particular, enabling this feature implies that WorkReuse should not be enabled.

Parameters:

inplaceUpdate (Any)
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#InplaceUpdateRequirement'

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

InplaceUpdateRequirement

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

class cwl_utils.parser.cwl_v1_1.ToolTimeLimit(timelimit, extension_fields=None, loadingOptions=None)

Bases: ProcessRequirement

Inheritance diagram of cwl_utils.parser.cwl_v1_1.ToolTimeLimit

Set an upper limit on the execution time of a CommandLineTool. A CommandLineTool whose execution duration exceeds the time limit may be preemptively terminated and considered failed. May also be used by batch systems to make scheduling decisions. The execution duration excludes external operations, such as staging of files, pulling a docker image etc, and only counts wall-time for the execution of the command line itself.

Parameters:

timelimit (Any)
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#ToolTimeLimit'

class_ = 'ToolTimeLimit'

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

ToolTimeLimit

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

class cwl_utils.parser.cwl_v1_1.ExpressionToolOutputParameter(type_, label=None, secondaryFiles=None, streamable=None, doc=None, id=None, format=None, extension_fields=None, loadingOptions=None)

Bases: OutputParameter

Inheritance diagram of cwl_utils.parser.cwl_v1_1.ExpressionToolOutputParameter

Define an input or output parameter to a process.

Parameters:

type_ (Any)
label (Optional[Any])
secondaryFiles (Optional[Any])
streamable (Optional[Any])
doc (Optional[Any])
id (Optional[Any])
format (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#ExpressionToolOutputParameter'

label = None

secondaryFiles = None

streamable = None

doc = None

id = None

format = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

ExpressionToolOutputParameter

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

class cwl_utils.parser.cwl_v1_1.WorkflowInputParameter(type_, label=None, secondaryFiles=None, streamable=None, doc=None, id=None, format=None, loadContents=None, loadListing=None, default=None, inputBinding=None, extension_fields=None, loadingOptions=None)

Bases: InputParameter

Inheritance diagram of cwl_utils.parser.cwl_v1_1.WorkflowInputParameter

Define an input or output parameter to a process.

Parameters:

type_ (Any)
label (Optional[Any])
secondaryFiles (Optional[Any])
streamable (Optional[Any])
doc (Optional[Any])
id (Optional[Any])
format (Optional[Any])
loadContents (Optional[Any])
loadListing (Optional[Any])
default (Optional[Any])
inputBinding (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#WorkflowInputParameter'

label = None

secondaryFiles = None

streamable = None

doc = None

id = None

format = None

loadContents = None

loadListing = None

default = None

type_

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 (LoadingOptions)
docRoot (Optional[str])

Return type:

WorkflowInputParameter

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

class cwl_utils.parser.cwl_v1_1.ExpressionTool(inputs, outputs, expression, id=None, label=None, doc=None, requirements=None, hints=None, cwlVersion=None, extension_fields=None, loadingOptions=None)

Bases: Process

Inheritance diagram of cwl_utils.parser.cwl_v1_1.ExpressionTool

An ExpressionTool is a type of Process object that can be run by itself or as a Workflow step. It executes a pure Javascript expression that has access to the same input parameters as a workflow. It is meant to be used sparingly as a way to isolate complex Javascript expressions that need to operate on input data and produce some result; perhaps just a rearrangement of the inputs. No Docker software container is required or allowed.

Parameters:

inputs (Any)
outputs (Any)
expression (Any)
id (Optional[Any])
label (Optional[Any])
doc (Optional[Any])
requirements (Optional[Any])
hints (Optional[Any])
cwlVersion (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#ExpressionTool'

id = None

label = None

doc = None

inputs

outputs

requirements = None

hints = None

cwlVersion = None

class_ = '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 (LoadingOptions)
docRoot (Optional[str])

Return type:

ExpressionTool

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

class cwl_utils.parser.cwl_v1_1.WorkflowOutputParameter(type_, label=None, secondaryFiles=None, streamable=None, doc=None, id=None, format=None, outputSource=None, linkMerge=None, extension_fields=None, loadingOptions=None)

Bases: OutputParameter

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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. It is legal to connect a WorkflowInputParameter to a WorkflowOutputParameter.

Parameters:

type_ (Any)
label (Optional[Any])
secondaryFiles (Optional[Any])
streamable (Optional[Any])
doc (Optional[Any])
id (Optional[Any])
format (Optional[Any])
outputSource (Optional[Any])
linkMerge (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#WorkflowOutputParameter'

label = None

secondaryFiles = None

streamable = None

doc = None

id = None

format = None

outputSource = None

linkMerge = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

WorkflowOutputParameter

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

class cwl_utils.parser.cwl_v1_1.Sink

Bases: Saveable

Inheritance diagram of cwl_utils.parser.cwl_v1_1.Sink

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

class cwl_utils.parser.cwl_v1_1.WorkflowStepInput(id=None, source=None, linkMerge=None, loadContents=None, loadListing=None, label=None, default=None, valueFrom=None, extension_fields=None, loadingOptions=None)

Bases: Identified, Sink, LoadContents, Labeled

Inheritance diagram of cwl_utils.parser.cwl_v1_1.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 process specified by the run field. Only input parameters declared by the target process will be passed through at runtime to the process though additonal parameters may be specified (for use within valueFrom expressions for instance) - unconnected or unused parameters do not represent an error condition.

## 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](#MultipleInputFeatureRequirement) must be specified in the workflow or workflow step requirements.

If the sink parameter is an array, or named in a [workflow scatter](#WorkflowStep) 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.

Parameters:

id (Optional[Any])
source (Optional[Any])
linkMerge (Optional[Any])
loadContents (Optional[Any])
loadListing (Optional[Any])
label (Optional[Any])
default (Optional[Any])
valueFrom (Optional[Any])
extension_fields (Optional[dict[str, Any]])
loadingOptions (Optional[LoadingOptions])

class_uri = 'https://w3id.org/cwl/cwl#WorkflowStepInput'

id = None

source = None

linkMerge = None

loadContents = None

loadListing = None

label = 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 (LoadingOptions)
docRoot (Optional[str])

Return type:

WorkflowStepInput

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:</