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Peter Amstutz
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Update examples to v1.0
1 parent 5403799 commit 156d28f

15 files changed

+72
-88
lines changed

‎v1.0/examples/1st-tool.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: echo
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inputs:
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- id: message
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message:
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type: string
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inputBinding:
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position: 1

‎v1.0/examples/1st-workflow.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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class: Workflow
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inputs:
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- id: inp
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type: File
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- id: ex
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type: string
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inp: File
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ex: string
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outputs:
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- id: classout
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classout:
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type: File
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source: "#compile/classfile"
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outputSource: "#compile/classfile"
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steps:
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- id: untar
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untar:
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run: tar-param.cwl
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inputs:
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- id: tarfile
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source: "#inp"
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- id: extractfile
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source: "#ex"
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outputs:
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- id: example_out
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tarfile: inp
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extractfile: ex
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outputs: [example_out]
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- id: compile
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compile:
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run: arguments.cwl
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inputs:
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- id: src
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source: "#untar/example_out"
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outputs:
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- id: classfile
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src: untar/example_out
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outputs: [classfile]

‎v1.0/examples/arguments.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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class: CommandLineTool
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label: Example trivial wrapper for Java 7 compiler
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baseCommand: javac
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hints:
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- class: DockerRequirement
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DockerRequirement:
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dockerPull: java:7
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baseCommand: javac
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arguments:
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- prefix: "-d"
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valueFrom: $(runtime.outdir)
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arguments: ["-d", $(runtime.outdir)]
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inputs:
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- id: src
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src:
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type: File
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inputBinding:
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position: 1
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outputs:
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- id: classfile
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classfile:
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type: File
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outputBinding:
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glob: "*.class"

‎v1.0/examples/array-inputs.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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class: CommandLineTool
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inputs:
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- id: filesA
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filesA:
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type:
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type: array
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items: string
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inputBinding:
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prefix: -A
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position: 1
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- id: filesB
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filesB:
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type:
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type: array
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items: string
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inputBinding:
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position: 2
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- id: filesC
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filesC:
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type:
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type: array
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items: string

‎v1.0/examples/array-outputs.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: touch
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inputs:
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- id: touchfiles
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touchfiles:
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type:
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type: array
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items: string
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inputBinding:
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position: 1
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outputs:
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- id: output
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output:
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type:
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type: array
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items: File

‎v1.0/examples/createfile.cwl

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class: CommandLineTool
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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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baseCommand: ["cat", "example.conf"]
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requirements:
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- class: CreateFileRequirement
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fileDef:
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- filename: example.conf
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fileContent: |
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CONFIGVAR=$(inputs.message)
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InitialWorkDirRequirirement:
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listing:
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example.conf: |
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CONFIGVAR=$(inputs.message)
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inputs:
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- id: message
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type: string
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message: string
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outputs: []

‎v1.0/examples/docker.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: node
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hints:
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- class: DockerRequirement
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DockerRequirement:
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dockerPull: node:slim
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inputs:
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- id: src
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src:
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type: File
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inputBinding:
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position: 1

‎v1.0/examples/env.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: env
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requirements:
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- class: EnvVarRequirement
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EnvVarRequirement:
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envDef:
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- envName: HELLO
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envValue: $(inputs.message)
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HELLO: $(inputs.message)
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inputs:
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- id: message
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type: string
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message: string
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outputs: []

‎v1.0/examples/expression.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: echo
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inputs: []
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outputs: []
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arguments:
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- valueFrom: $(1+1)
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prefix: -A
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- valueFrom: $("/foo/bar/baz".split('/').slice(-1)[0])
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prefix: -B
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- valueFrom: |
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- prefix: -A
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valueFrom: $(1+1)
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- prefix: -B
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valueFrom: $("/foo/bar/baz".split('/').slice(-1)[0])
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- prefix: -C
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valueFrom: |
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${
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var r = [];
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for (var i = 10; i >= 1; i--) {
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r.push(i);
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}
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return r;
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}
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prefix: -C

‎v1.0/examples/inp.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: echo
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inputs:

‎v1.0/examples/linkfile.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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class: CommandLineTool
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hints:
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- class: DockerRequirement
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DockerRequirement:
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dockerPull: java:7
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baseCommand: javac
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requirements:
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- class: InlineJavascriptRequirement
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- class: CreateFileRequirement
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fileDef:
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- filename: $(inputs.src.path.split('/').slice(-1)[0])
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fileContent: $(inputs.src)
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- class: InitialWorkDirRequirirement
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listing:
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- $(inputs.src)
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inputs:
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- id: src
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src:
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type: File
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inputBinding:
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position: 1
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valueFrom: $(inputs.src.path.split('/').slice(-1)[0])
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valueFrom: $(inputs.src.basename)
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outputs:
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- id: classfile
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classfile:
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type: File
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outputBinding:
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glob: "*.class"

‎v1.0/examples/record.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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class: CommandLineTool
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inputs:
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- id: dependent_parameters
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dependent_parameters:
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type:
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type: record
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name: dependent_parameters
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fields:
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- name: itemA
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itemA:
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type: string
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inputBinding:
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prefix: -A
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- name: itemB
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itemB:
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type: string
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inputBinding:
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prefix: -B
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- id: exclusive_parameters
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exclusive_parameters:
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type:
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- type: record
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name: itemC
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fields:
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- name: itemC
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itemC:
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type: string
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inputBinding:
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prefix: -C
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- type: record
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name: itemD
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fields:
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- name: itemD
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itemD:
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type: string
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inputBinding:
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prefix: -D

‎v1.0/examples/stdout.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: echo
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stdout: output.txt
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inputs:
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- id: message
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message:
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type: string
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inputBinding:
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position: 1
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outputs:
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- id: output
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type: File
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outputBinding:
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glob: output.txt
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type: stdout

‎v1.0/examples/tar-param.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: [tar, xf]
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inputs:
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- id: tarfile
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tarfile:
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type: File
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inputBinding:
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position: 1
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- id: extractfile
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extractfile:
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type: string
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inputBinding:
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position: 2
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outputs:
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- id: example_out
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example_out:
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type: File
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outputBinding:
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glob: $(inputs.extractfile)

‎v1.0/examples/tar.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: [tar, xf]
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inputs:
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- id: tarfile
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tarfile:
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type: File
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inputBinding:
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position: 1
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outputs:
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- id: example_out
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example_out:
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type: File
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outputBinding:
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glob: hello.txt

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