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Squashed 'cwltool/schemas/' changes from 36b3da1..1550753
1550753 Merge pull request #302 from common-workflow-language/build-v1.1.0-dev1-pages 09d3412 build v1.1.0-dev1 webpages 1318a55 rename draft-4 to v1.0.0 in site/ f188887 Merge pull request #301 from common-workflow-language/fix-stdin-tests d71528d fix stdin shortcut tests 6fc30e1 Merge pull request #300 from common-workflow-language/stdin-shortcut REVERT: 36b3da1 put stdin type in correct place git-subtree-dir: cwltool/schemas git-subtree-split: 1550753
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‎site/cwlsite-job.json

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‎site/cwlsite-job.yaml

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#!/usr/bin/env cwl-runner
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brand: CWL
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brandimg: {class: File, path: CWL-Logo-Header.png}
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cwl:tool: cwlsite.cwl
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render:
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- brandimg: '<img src=''CWL-Logo-Header.png'' style=''height: 61px; margin-top: -20px;
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margin-left: -20px''></img>'
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brandlink: index.html
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primtype: null
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redirect: []
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renderlist: []
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source: {class: File, path: ../README.md}
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target: index.html
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- {$import: cwlsite-draft3-job.json}
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- {$import: cwlsite-v1.0.0-job.json}
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- {$import: cwlsite-v1.1.0-dev1-job.yaml}
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schemas:
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- {$import: cwlsite-draft3-schemas.json}
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- {$import: cwlsite-v1.0.0-schemas.json}
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- {$import: cwlsite-v1.1.0-dev1-schemas.yaml}

‎site/cwlsite-draft4-job.json renamed to ‎site/cwlsite-v1.0.0-job.json

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"source": {
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"class": "File",
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"path": "../v1.0/CommandLineTool-standalone.yml",
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"secondaryFiles": {"$import": "draft4-deps.json"}
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"secondaryFiles": {"$import": "v1.0.0-deps.json"}
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},
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"target": "v1.0/CommandLineTool.html",
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"renderlist": [
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"source": {
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"class": "File",
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"path": "../v1.0/CommonWorkflowLanguage.yml",
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"secondaryFiles": {"$import": "draft4-deps.json"}
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"secondaryFiles": {"$import": "v1.0.0-deps.json"}
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},
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"target": "v1.0/Workflow.html",
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"renderlist": [
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"primtype": "#CWLType"
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},
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{
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"source": {$import: draft4-metaschema.json},
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"source": {$import: v1.0.0-metaschema.json},
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"target": "v1.0/SchemaSalad.html",
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"renderlist": [
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"https://w3id.org/cwl/salad#Semantic_Annotations_for_Linked_Avro_Data",

‎site/cwlsite-draft4-schemas.json renamed to ‎site/cwlsite-v1.0.0-schemas.json

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"schema_in": {
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"class": "File",
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"path": "../v1.0/CommonWorkflowLanguage.yml",
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"secondaryFiles": {"$import": "draft4-deps.json"}
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"secondaryFiles": {"$import": "v1.0.0-deps.json"}
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},
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"context_target": "v1.0/cwl-context.json",
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"rdfs_target": "v1.0/cwl.ttl"
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}, {
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"schema_in": {$import: draft4-metaschema.json},
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"schema_in": {$import: v1.0.0-metaschema.json},
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"context_target": "v1.0/salad-context.json",
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"rdfs_target": "v1.0/salad.ttl"
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}

‎site/cwlsite-v1.1.0-dev1-job.yaml

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- brandimg: '<img src=''../CWL-Logo-Header.png'' style=''height: 61px; margin-top:
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-20px; margin-left: -20px''></img>'
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brandlink: ../index.html
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primtype: null
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redirect: []
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renderlist: []
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source: {class: File, path: ../v1.1.0-dev1/README.md}
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target: v1.1.0-dev1/index.html
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- brandimg: '<img src=''../CWL-Logo-Header.png'' style=''height: 61px; margin-top:
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-20px; margin-left: -20px''></img>'
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brandlink: index.html
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primtype: '#CWLType'
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redirect: []
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renderlist: ['https://w3id.org/cwl/cwl#CommandLineToolDoc', 'https://w3id.org/cwl/cwl#CommandLineTool']
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source:
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class: File
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path: ../v1.1.0-dev1/CommandLineTool-standalone.yml
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secondaryFiles: {$import: v1.1.0-dev1-deps.yaml}
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target: v1.1.0-dev1/CommandLineTool.html
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- brandimg: '<img src=''../CWL-Logo-Header.png'' style=''height: 61px; margin-top:
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-20px; margin-left: -20px''></img>'
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brandlink: index.html
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primtype: '#CWLType'
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redirect: ['https://w3id.org/cwl/cwl#CommandLineTool=CommandLineTool.html#CommandLineTool',
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'https://w3id.org/cwl/cwl#DockerRequirement=CommandLineTool.html#DockerRequirement',
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'https://w3id.org/cwl/cwl#CreateFileRequirement=CommandLineTool.html#CreateFileRequirement',
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'https://w3id.org/cwl/cwl#EnvVarRequirement=CommandLineTool.html#EnvVarRequirement',
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'https://w3id.org/cwl/cwl#ShellCommandRequirement=CommandLineTool.html#ShellCommandRequirement',
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'https://w3id.org/cwl/cwl#ResourceRequirement=CommandLineTool.html#ResourceRequirement']
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renderlist: ['https://w3id.org/cwl/cwl#WorkflowDoc', 'https://w3id.org/cwl/cwl#Workflow']
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source:
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class: File
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path: ../v1.1.0-dev1/CommonWorkflowLanguage.yml
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secondaryFiles: {$import: v1.1.0-dev1-deps.yaml}
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target: v1.1.0-dev1/Workflow.html
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- brandimg: '<img src=''../CWL-Logo-Header.png'' style=''height: 61px; margin-top:
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-20px; margin-left: -20px''></img>'
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brandlink: index.html
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primtype: null
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redirect: []
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renderlist: ['https://w3id.org/cwl/salad#Semantic_Annotations_for_Linked_Avro_Data',
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'https://w3id.org/cwl/salad#SaladRecordSchema', 'https://w3id.org/cwl/salad#SaladEnumSchema',
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'https://w3id.org/cwl/salad#Documentation']
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source: {$import: v1.1.0-dev1-metaschema.yaml}
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target: v1.1.0-dev1/SchemaSalad.html
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- brandimg: '<img src=''../CWL-Logo-Header.png'' style=''height: 61px; margin-top:
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-20px; margin-left: -20px''></img>'
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brandlink: index.html
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primtype: null
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redirect: []
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renderlist: []
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source: {$import: userguide-v1.1.0-dev1-input.yaml}
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target: v1.1.0-dev1/UserGuide.html

‎site/cwlsite-v1.1.0-dev1-schemas.yaml

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- context_target: v1.1.0-dev1/cwl-context.json
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rdfs_target: v1.1.0-dev1/cwl.ttl
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schema_in:
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class: File
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path: ../v1.1.0-dev1/CommonWorkflowLanguage.yml
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secondaryFiles: {$import: v1.1.0-dev1-deps.yaml}
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- context_target: v1.1.0-dev1/salad-context.json
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rdfs_target: v1.1.0-dev1/salad.ttl
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schema_in: {$import: v1.1.0-dev1-metaschema.yaml}

‎site/userguide-v1.1.0-dev1-input.yaml

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class: File
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location: ../v1.1.0-dev1/UserGuide.yml
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secondaryFiles:
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- {basename: userguide-intro.md, class: File, location: ../v1.1.0-dev1/userguide-intro.md}
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- basename: examples
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class: Directory
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listing:
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- {basename: record-job1.yml, class: File, location: ../v1.1.0-dev1/examples/record-job1.yml}
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- {basename: expression.cwl, class: File, location: ../v1.1.0-dev1/examples/expression.cwl}
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- {basename: array-outputs-job.yml, class: File, location: ../v1.1.0-dev1/examples/array-outputs-job.yml}
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- {basename: tar-param.cwl, class: File, location: ../v1.1.0-dev1/examples/tar-param.cwl}
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- {basename: inp-job.yml, class: File, location: ../v1.1.0-dev1/examples/inp-job.yml}
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- {basename: 1st-workflow-job.yml, class: File, location: ../v1.1.0-dev1/examples/1st-workflow-job.yml}
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- {basename: record-job2.yml, class: File, location: ../v1.1.0-dev1/examples/record-job2.yml}
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- {basename: record-job3.yml, class: File, location: ../v1.1.0-dev1/examples/record-job3.yml}
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- {basename: echo-job.yml, class: File, location: ../v1.1.0-dev1/examples/echo-job.yml}
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- {basename: array-outputs.cwl, class: File, location: ../v1.1.0-dev1/examples/array-outputs.cwl}
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- {basename: array-inputs-job.yml, class: File, location: ../v1.1.0-dev1/examples/array-inputs-job.yml}
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- {basename: 1st-workflow.cwl, class: File, location: ../v1.1.0-dev1/examples/1st-workflow.cwl}
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- {basename: docker.cwl, class: File, location: ../v1.1.0-dev1/examples/docker.cwl}
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- {basename: stdout.cwl, class: File, location: ../v1.1.0-dev1/examples/stdout.cwl}
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- {basename: docker-job.yml, class: File, location: ../v1.1.0-dev1/examples/docker-job.yml}
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- {basename: tar.cwl, class: File, location: ../v1.1.0-dev1/examples/tar.cwl}
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- {basename: createfile.cwl, class: File, location: ../v1.1.0-dev1/examples/createfile.cwl}
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- {basename: 1st-tool.cwl, class: File, location: ../v1.1.0-dev1/examples/1st-tool.cwl}
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- {basename: env.cwl, class: File, location: ../v1.1.0-dev1/examples/env.cwl}
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- {basename: arguments-job.yml, class: File, location: ../v1.1.0-dev1/examples/arguments-job.yml}
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- {basename: tar-param-job.yml, class: File, location: ../v1.1.0-dev1/examples/tar-param-job.yml}
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- {basename: array-inputs.cwl, class: File, location: ../v1.1.0-dev1/examples/array-inputs.cwl}
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- {basename: inp.cwl, class: File, location: ../v1.1.0-dev1/examples/inp.cwl}
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- {basename: arguments.cwl, class: File, location: ../v1.1.0-dev1/examples/arguments.cwl}
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- {basename: linkfile.cwl, class: File, location: ../v1.1.0-dev1/examples/linkfile.cwl}
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- {basename: record.cwl, class: File, location: ../v1.1.0-dev1/examples/record.cwl}
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- {basename: tar-job.yml, class: File, location: ../v1.1.0-dev1/examples/tar-job.yml}
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location: _:4f9d886b-443f-49bd-8e0e-f3517a8a5c34

‎site/draft4-deps.json renamed to ‎site/v1.0.0-deps.json

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‎site/draft4-metaschema.json renamed to ‎site/v1.0.0-metaschema.json

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‎site/v1.1.0-dev1-deps.yaml

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- basename: Process.yml
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class: File
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location: ../v1.1.0-dev1/Process.yml
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secondaryFiles:
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- {basename: concepts.md, class: File, location: ../v1.1.0-dev1/concepts.md}
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- basename: salad
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class: Directory
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listing:
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- basename: schema_salad
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class: Directory
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listing:
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- basename: metaschema
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class: Directory
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listing:
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- {basename: metaschema_base.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/metaschema_base.yml}
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location: _:8d932277-54ee-49f7-b7b3-007108151ed4
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location: _:31c5c0f1-dfcb-4a68-a5e1-063d03e85d3a
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location: _:4a097285-861e-42ac-9322-20244d69dc96
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- basename: CommandLineTool.yml
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class: File
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location: ../v1.1.0-dev1/CommandLineTool.yml
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secondaryFiles:
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- {basename: contrib.md, class: File, location: ../v1.1.0-dev1/contrib.md}
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- {basename: concepts.md, class: File, location: ../v1.1.0-dev1/concepts.md}
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- {basename: invocation.md, class: File, location: ../v1.1.0-dev1/invocation.md}
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- {basename: intro.md, class: File, location: ../v1.1.0-dev1/intro.md}
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- basename: Workflow.yml
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class: File
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location: ../v1.1.0-dev1/Workflow.yml
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secondaryFiles:
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- {basename: contrib.md, class: File, location: ../v1.1.0-dev1/contrib.md}
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- {basename: concepts.md, class: File, location: ../v1.1.0-dev1/concepts.md}
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- {basename: intro.md, class: File, location: ../v1.1.0-dev1/intro.md}

‎site/v1.1.0-dev1-metaschema.yaml

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class: File
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location: ../v1.1.0-dev1/salad/schema_salad/metaschema/metaschema.yml
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secondaryFiles:
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- basename: link_res.yml
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class: File
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location: ../v1.1.0-dev1/salad/schema_salad/metaschema/link_res.yml
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secondaryFiles:
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- {basename: link_res_schema.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/link_res_schema.yml}
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- {basename: link_res_src.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/link_res_src.yml}
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- {basename: link_res_proc.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/link_res_proc.yml}
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- {basename: salad.md, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/salad.md}
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- {basename: metaschema_base.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/metaschema_base.yml}
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- {basename: import_include.md, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md}
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- basename: field_name.yml
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class: File
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location: ../v1.1.0-dev1/salad/schema_salad/metaschema/field_name.yml
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secondaryFiles:
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- {basename: field_name_src.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/field_name_src.yml}
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- {basename: field_name_schema.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/field_name_schema.yml}
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- {basename: field_name_proc.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/field_name_proc.yml}
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- basename: ident_res.yml
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class: File
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location: ../v1.1.0-dev1/salad/schema_salad/metaschema/ident_res.yml
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secondaryFiles:
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- {basename: ident_res_proc.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/ident_res_proc.yml}
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- {basename: ident_res_schema.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/ident_res_schema.yml}
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- {basename: ident_res_src.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/ident_res_src.yml}
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- basename: vocab_res.yml
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class: File
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location: ../v1.1.0-dev1/salad/schema_salad/metaschema/vocab_res.yml
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secondaryFiles:
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- {basename: vocab_res_schema.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/vocab_res_schema.yml}
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- {basename: vocab_res_proc.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/vocab_res_proc.yml}
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- {basename: vocab_res_src.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/vocab_res_src.yml}

‎v1.1.0-dev1/CommandLineTool.yml

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extends: InputParameter
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doc: An input parameter for a CommandLineTool.
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specialize:
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- specializeFrom: InputRecordSchema
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specializeTo: CommandInputRecordSchema
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- specializeFrom: InputEnumSchema
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specializeTo: CommandInputEnumSchema
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- specializeFrom: InputArraySchema
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specializeTo: CommandInputArraySchema
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- specializeFrom: InputBinding
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specializeTo: CommandLineBinding
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fields:
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- name: type
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type:
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- "null"
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- CWLType
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- stdin
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- CommandInputRecordSchema
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- CommandInputEnumSchema
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- CommandInputArraySchema
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- string
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- type: array
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items:
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- CWLType
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- CommandInputRecordSchema
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- CommandInputEnumSchema
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- CommandInputArraySchema
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jsonldPredicate:
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"_id": "sld:type"
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refScope: 2
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typeDSL: True
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Specify valid types of data that may be assigned to this parameter.
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docParent: "#CommandOutputParameter"
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Only valid as a `type` for a `CommandLineTool` input with no
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`inputBinding` set. `stdin` must not be specified at the `CommandLineTool`

‎v1.1.0-dev1/Process.yml

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The default value for this parameter if not provided in the input
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object.
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type:
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- CWLType
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- InputRecordSchema
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- InputEnumSchema
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- InputArraySchema
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items:
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- CWLType
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- InputRecordSchema
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- InputEnumSchema
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- InputArraySchema
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- string
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"_type": "@vocab"
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refScope: 2
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typeDSL: True
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doc: |
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Specify valid types of data that may be assigned to this parameter.
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- name: OutputParameter
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‎v1.1.0-dev1/Workflow.yml

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Specify valid types of data that may be assigned to this parameter.
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- name: RegularInputParameter
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type: record
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extends: InputParameter
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fields:
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- name: type
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type:
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- "null"
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- CWLType
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- InputRecordSchema
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- InputEnumSchema
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- InputArraySchema
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- string
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items:
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- CWLType
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- InputRecordSchema
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- InputEnumSchema
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- InputArraySchema
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- string
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"_id": "sld:type"
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"_type": "@vocab"
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refScope: 2
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doc: |
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Specify valid types of data that may be assigned to this parameter.
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name: ExpressionTool
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extends: Process
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specialize:
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- specializeFrom: "#InputParameter"
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extends: "#Process"
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specialize:
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- specializeFrom: "#InputParameter"
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specializeTo: "#RegularInputParameter"
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- specializeFrom: "#OutputParameter"
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specializeTo: "#WorkflowOutputParameter"
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doc: |

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