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Peter Amstutz
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Squashed 'cwltool/schemas/' changes from b3d54b7..2ec0b1b
2ec0b1b Update tests. Add 'doc' field to Parameter because it doesn't inherit from salad Record. git-subtree-dir: cwltool/schemas git-subtree-split: 2ec0b1b
1 parent ec6713e commit 0035ef0

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‎v1.0/Process.yml

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indicate whether it is valid to stream file contents using a named
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pipe. Default: `false`.
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- name: doc
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type:
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- string?
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- string[]?
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doc: "A documentation string for this type, or an array of strings which should be concatenated."
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jsonldPredicate: "rdfs:comment"
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- type: enum
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name: Expression

‎v1.0/v1.0/cat1-testcli.cwl

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{
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"class": "CommandLineTool",
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"cwlVersion": "v1.0.dev4",
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"description": "Print the contents of a file to stdout using 'cat' running in a docker container.",
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"doc": "Print the contents of a file to stdout using 'cat' running in a docker container.",
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"inputs": [
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{
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"id": "file1",

‎v1.0/v1.0/cat1-tool.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: v1.0.dev4
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class: CommandLineTool
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
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hints:
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DockerRequirement:
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dockerPull: debian:wheezy

‎v1.0/v1.0/cat2-tool.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.0.dev4
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
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hints:
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DockerRequirement:
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dockerPull: debian:wheezy

‎v1.0/v1.0/cat3-tool-mediumcut.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.0.dev4
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
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hints:
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DockerRequirement:
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dockerPull: debian:wheezy
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inputs:
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file1:
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type: File
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label: Input File
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description: "The file that will be copied using 'cat'"
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doc: "The file that will be copied using 'cat'"
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inputBinding: {position: 1}
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outputs:
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output_file:

‎v1.0/v1.0/cat3-tool-shortcut.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.0.dev4
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
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hints:
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DockerRequirement:
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dockerPull: debian:wheezy
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inputs:
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file1:
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type: File
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label: Input File
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description: "The file that will be copied using 'cat'"
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doc: "The file that will be copied using 'cat'"
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inputBinding: {position: 1}
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outputs:
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output_file:

‎v1.0/v1.0/cat3-tool.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.0.dev4
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
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hints:
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DockerRequirement:
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dockerPull: debian:wheezy
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inputs:
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file1:
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type: File
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label: Input File
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description: "The file that will be copied using 'cat'"
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doc: "The file that will be copied using 'cat'"
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inputBinding: {position: 1}
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outputs:
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output_file:

‎v1.0/v1.0/cat4-tool.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.0.dev4
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
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hints:
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DockerRequirement:
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dockerPull: debian:wheezy

‎v1.0/v1.0/cat5-tool.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: v1.0.dev4
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class: CommandLineTool
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
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hints:
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DockerRequirement:
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dockerPull: "debian:wheezy"
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file1:
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type: File
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label: "Input File"
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description: "The file that will be copied using 'cat'"
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doc: "The file that will be copied using 'cat'"
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inputBinding: {position: 1}
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outputs:
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output_file:

‎v1.0/v1.0/egrep-stderr-mediumcut.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.0.dev4
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description: "Test of capturing stderr output in a docker container."
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doc: "Test of capturing stderr output in a docker container."
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hints:
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DockerRequirement:
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dockerPull: debian:wheezy

‎v1.0/v1.0/egrep-stderr-shortcut.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.0.dev4
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description: "Test of capturing stderr output in a docker container."
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doc: "Test of capturing stderr output in a docker container."
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hints:
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DockerRequirement:
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dockerPull: debian:wheezy

‎v1.0/v1.0/egrep-stderr.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.0.dev4
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description: "Test of capturing stderr output in a docker container."
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doc: "Test of capturing stderr output in a docker container."
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hints:
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DockerRequirement:
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dockerPull: debian:wheezy

‎v1.0/v1.0/formattest.cwl

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edam: "http://edamontology.org/"
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cwlVersion: v1.0.dev4
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class: CommandLineTool
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description: "Reverse each line using the `rev` command"
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doc: "Reverse each line using the `rev` command"
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inputs:
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input:
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type: File

‎v1.0/v1.0/formattest2.cwl

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- EDAM.owl
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class: CommandLineTool
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cwlVersion: v1.0.dev4
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description: "Reverse each line using the `rev` command"
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doc: "Reverse each line using the `rev` command"
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inputs:
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input:

‎v1.0/v1.0/formattest3.cwl

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- gx_edam.ttl
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class: CommandLineTool
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cwlVersion: v1.0.dev4
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description: "Reverse each line using the `rev` command"
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doc: "Reverse each line using the `rev` command"
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inputs:
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input:

‎v1.0/v1.0/metadata.cwl

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cwlVersion: v1.0.dev4
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class: CommandLineTool
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
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dct:creator:
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id: "http://orcid.org/0000-0003-3566-7705"

‎v1.0/v1.0/optional-output.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: "v1.0.dev4"
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
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hints:
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DockerRequirement:
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dockerPull: debian:wheezy
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inputs:
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file1:
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type: File
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label: Input File
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description: "The file that will be copied using 'cat'"
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doc: "The file that will be copied using 'cat'"
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inputBinding: {position: 1}
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outputs:
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output_file:

‎v1.0/v1.0/revsort.cwl

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# This is a two-step workflow which uses "revtool" and "sorttool" defined above.
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#
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class: Workflow
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description: "Reverse the lines in a document, then sort those lines."
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doc: "Reverse the lines in a document, then sort those lines."
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cwlVersion: v1.0.dev4
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# Requirements & hints specify prerequisites and extensions to the workflow.
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inputs:
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input:
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type: File
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description: "The input file to be processed."
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doc: "The input file to be processed."
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reverse_sort:
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type: boolean
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default: true
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description: "If true, reverse (decending) sort"
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doc: "If true, reverse (decending) sort"
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# The "outputs" array defines the structure of the output object that describes
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# the outputs of the workflow.
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output:
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type: File
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outputSource: sorted/output
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description: "The output with the lines reversed and sorted."
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doc: "The output with the lines reversed and sorted."
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# The "steps" array lists the executable steps that make up the workflow.
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# The tool to execute each step is listed in the "run" field.

‎v1.0/v1.0/revtool.cwl

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#
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class: CommandLineTool
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cwlVersion: v1.0.dev4
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description: "Reverse each line using the `rev` command"
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doc: "Reverse each line using the `rev` command"
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# The "inputs" array defines the structure of the input object that describes
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# the inputs to the underlying program. Here, there is one input field

‎v1.0/v1.0/shelltest.cwl

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class: CommandLineTool
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cwlVersion: v1.0.dev4
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description: "Reverse each line using the `rev` command then sort."
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doc: "Reverse each line using the `rev` command then sort."
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requirements:
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- class: ShellCommandRequirement
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inputs:

‎v1.0/v1.0/sorttool.cwl

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# Example command line program wrapper for the Unix tool "sort"
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# demonstrating command line flags.
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class: CommandLineTool
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description: "Sort lines using the `sort` command"
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doc: "Sort lines using the `sort` command"
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cwlVersion: v1.0.dev4
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# This example is similar to the previous one, with an additional input

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