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149 changes: 79 additions & 70 deletions CommandLineTool.yml
Original file line number Diff line number Diff line change
Expand Up @@ -650,75 +650,6 @@ $graph:
- specializeFrom: OutputArraySchema
specializeTo: CommandOutputArraySchema


- type: record
name: CommandInputParameter
extends: InputParameter
doc: An input parameter for a CommandLineTool.
fields:
- name: type
type:
- CWLType
- stdin
- CommandInputRecordSchema
- CommandInputEnumSchema
- CommandInputArraySchema
- string
- type: array
items:
- CWLType
- CommandInputRecordSchema
- CommandInputEnumSchema
- CommandInputArraySchema
- string
jsonldPredicate:
"_id": "sld:type"
"_type": "@vocab"
refScope: 2
typeDSL: True
doc: |
Specify valid types of data that may be assigned to this parameter.
- name: inputBinding
type: CommandLineBinding?
doc: |
Describes how to turn the input parameters of a process into
command line arguments.
jsonldPredicate: "cwl:inputBinding"

- type: record
name: CommandOutputParameter
extends: OutputParameter
doc: An output parameter for a CommandLineTool.
fields:
- name: type
type:
- CWLType
- stdout
- stderr
- CommandOutputRecordSchema
- CommandOutputEnumSchema
- CommandOutputArraySchema
- string
- type: array
items:
- CWLType
- CommandOutputRecordSchema
- CommandOutputEnumSchema
- CommandOutputArraySchema
- string
jsonldPredicate:
"_id": "sld:type"
"_type": "@vocab"
refScope: 2
typeDSL: True
doc: |
Specify valid types of data that may be assigned to this parameter.
- name: outputBinding
type: CommandOutputBinding?
jsonldPredicate: "cwl:outputBinding"
doc: Describes how to generate this output object based on the files
produced by a CommandLineTool

- name: stdin
type: enum
symbols: [ "cwl:stdin" ]
Expand Down Expand Up @@ -795,7 +726,6 @@ $graph:
(e.g. `echo a && echo b`) `stdout` must include the output of
every command.


- name: stderr
type: enum
symbols: [ "cwl:stderr" ]
Expand Down Expand Up @@ -843,6 +773,85 @@ $graph:
stderr: random_stderr_filenameABCDEFG
```

- name: CommandInputParameterType
type: union
names:
- CWLType
- stdin
- CommandInputRecordSchema
- CommandInputEnumSchema
- CommandInputArraySchema
- string
- type: array
items:
- CWLType
- CommandInputRecordSchema
- CommandInputEnumSchema
- CommandInputArraySchema
- string
doc: |
Type schema for the CWL `CommandInputParameter` class.

- type: record
name: CommandInputParameter
extends: InputParameter
doc: An input parameter for a CommandLineTool.
fields:
- name: type
type: CommandInputParameterType
jsonldPredicate:
"_id": "sld:type"
"_type": "@vocab"
refScope: 2
typeDSL: True
doc: |
Specify valid types of data that may be assigned to this parameter.
- name: inputBinding
type: CommandLineBinding?
doc: |
Describes how to turn the input parameters of a process into
command line arguments.
jsonldPredicate: "cwl:inputBinding"

- name: CommandOutputParameterType
type: union
names:
- CWLType
- stdout
- stderr
- CommandOutputRecordSchema
- CommandOutputEnumSchema
- CommandOutputArraySchema
- string
- type: array
items:
- CWLType
- CommandOutputRecordSchema
- CommandOutputEnumSchema
- CommandOutputArraySchema
- string
doc: |
Type schema for the CWL `CommandInputParameter` class.

- type: record
name: CommandOutputParameter
extends: OutputParameter
doc: An output parameter for a CommandLineTool.
fields:
- name: type
type: CommandOutputParameterType
jsonldPredicate:
"_id": "sld:type"
"_type": "@vocab"
refScope: 2
typeDSL: True
doc: |
Specify valid types of data that may be assigned to this parameter.
- name: outputBinding
type: CommandOutputBinding?
jsonldPredicate: "cwl:outputBinding"
doc: Describes how to generate this output object based on the files
produced by a CommandLineTool

- type: record
name: CommandLineTool
Expand Down
28 changes: 2 additions & 26 deletions Operation.yml
Original file line number Diff line number Diff line change
Expand Up @@ -14,19 +14,7 @@ $graph:
Describe an input parameter of an operation.
fields:
- name: type
type:
- CWLType
- InputRecordSchema
- InputEnumSchema
- InputArraySchema
- string
- type: array
items:
- CWLType
- InputRecordSchema
- InputEnumSchema
- InputArraySchema
- string
type: InputParameterType
jsonldPredicate:
"_id": "sld:type"
"_type": "@vocab"
Expand All @@ -43,19 +31,7 @@ $graph:
Describe an output parameter of an operation.
fields:
- name: type
type:
- CWLType
- OutputRecordSchema
- OutputEnumSchema
- OutputArraySchema
- string
- type: array
items:
- CWLType
- OutputRecordSchema
- OutputEnumSchema
- OutputArraySchema
- string
type: OutputParameterType
jsonldPredicate:
"_id": "sld:type"
"_type": "@vocab"
Expand Down
36 changes: 36 additions & 0 deletions Process.yml
Original file line number Diff line number Diff line change
Expand Up @@ -320,6 +320,24 @@ $graph:
- specializeFrom: "sld:PrimitiveType"
specializeTo: CWLType

- name: InputParameterType
type: union
names:
- CWLType
- InputRecordSchema
- InputEnumSchema
- InputArraySchema
- string
- type: array
items:
- CWLType
- InputRecordSchema
- InputEnumSchema
- InputArraySchema
- string
doc: |
Type schema for the CWL `WorkflowInputParameter` and
`OperationInputParameter` classes.

- name: OutputRecordField
type: record
Expand Down Expand Up @@ -364,6 +382,24 @@ $graph:
- specializeFrom: "sld:PrimitiveType"
specializeTo: CWLType

- name: OutputParameterType
type: union
names:
- CWLType
- OutputRecordSchema
- OutputEnumSchema
- OutputArraySchema
- string
- type: array
items:
- CWLType
- OutputRecordSchema
- OutputEnumSchema
- OutputArraySchema
- string
doc: |
Type schema for the CWL `WorkflowOutputParameter` and
`OperationOutputParameter` classes.

- name: InputParameter
type: record
Expand Down
28 changes: 2 additions & 26 deletions Workflow.yml
Original file line number Diff line number Diff line change
Expand Up @@ -294,19 +294,7 @@ $graph:
docParent: "#Workflow"
fields:
- name: type
type:
- CWLType
- InputRecordSchema
- InputEnumSchema
- InputArraySchema
- string
- type: array
items:
- CWLType
- InputRecordSchema
- InputEnumSchema
- InputArraySchema
- string
type: InputParameterType
jsonldPredicate:
"_id": "sld:type"
"_type": "@vocab"
Expand Down Expand Up @@ -418,19 +406,7 @@ $graph:
The method to use to choose non-null elements among multiple sources.

- name: type
type:
- CWLType
- OutputRecordSchema
- OutputEnumSchema
- OutputArraySchema
- string
- type: array
items:
- CWLType
- OutputRecordSchema
- OutputEnumSchema
- OutputArraySchema
- string
type: OutputParameterType
jsonldPredicate:
"_id": "sld:type"
"_type": "@vocab"
Expand Down
2 changes: 1 addition & 1 deletion extensions.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ $namespaces:
cwl: "https://w3id.org/cwl/cwl#"
cwltool: "http://commonwl.org/cwltool#"
$graph:
- $import: https://github.com/common-workflow-language/cwl-v1.2/raw/codegen/CommonWorkflowLanguage.yml
- $import: CommonWorkflowLanguage.yml

- name: Secrets
type: record
Expand Down
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