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‎cwltool/schemas/README.md

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[![GitHub stars](https://img.shields.io/github/stars/common-workflow-language/common-workflow-language.svg)](https://github.com/common-workflow-language/common-workflow-language/stargazers) [![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/common-workflow-language/common-workflow-language?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [**Support**](#Support)
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<a href="https://www.youtube.com/watch?v=86eY8xs-Vo8"><img align="right" src="https://github.com/common-workflow-language/logo/raw/master/intro_video_screenshot_413x193.png" alt="[Video] Common Workflow Language explained in 64 seconds"></a>
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The Common Workflow Language (CWL) is a specification for describing analysis
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workflows and tools in a way that makes them portable and scalable across a
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variety of software and hardware environments, from workstations to cluster,
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cloud, and high performance computing (HPC) environments. CWL is designed to
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meet the needs of data-intensive science, such as Bioinformatics, Medical
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Imaging, Astronomy, Physics, and Chemistry.
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<a href="https://open-stand.org/about-us/principles"><img align="left" src="http://standards.ieee.org/images/openstand/128x128-blue2.png" alt="Open Stand badge"></a>
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CWL is developed by an informal, multi-vendor working group consisting of
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organizations and individuals aiming to enable scientists to share data
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analysis workflows. [The CWL project is on Github](https://github.com/common-workflow-language/common-workflow-language) and we follow the [Open-Stand.org principles for collaborative open standards development](https://open-stand.org/about-us/principles/)
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[![Open Stand badge](http://standards.ieee.org/images/openstand/128x128-blue2.png)](https://open-stand.org/about-us/principles/).
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CWL builds on technologies such as [JSON-LD](http://json-ld.org)
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for data modeling and [Docker](http://docker.com) for portable runtime
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For developers and advanced users, the current
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[CWL specification (v1.0)](http://www.commonwl.org/v1.0/) provides
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authoritative documentation of the execution of CWL documents. Links older
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drafts:
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[draft-1](https://github.com/common-workflow-language/common-workflow-language/tree/master/draft-1),
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[draft-2](http://www.commonwl.org/draft-2/),
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[draft-3](http://www.commonwl.org/draft-3/)
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authoritative documentation of the execution of CWL documents.
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### Citation
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Please cite https://dx.doi.org/10.6084/m9.figshare.3115156.v2
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* [Institute for Systems Biology](https://www.systemsbiology.org/)
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* [ELIXIR Europe](https://www.elixir-europe.org/)
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* [BioExcel CoE](http://bioexcel.eu/)
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* [BD2K](https://commonfund.nih.gov/bd2k)
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## Individual Contributors
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‎cwltool/schemas/doc/cli-description-languages-comparison.md

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# Comparison of Command Line Interface description languages
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## Compared languages
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* Galaxy v17.05: https://github.com/galaxyproject/galaxy/blob/release_17.05/lib/galaxy/tools/xsd/galaxy.xsd
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* CTD v1.7.0 : https://github.com/WorkflowConversion/CTDSchema/blob/Version_1_7_0/CTD.xsd
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* CWL v1.0: http://www.commonwl.org/v1.0/CommandLineTool.html / https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/CommandLineTool.yml
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## Summary
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### Tool description
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CTD reflects the perspective of a tool author targetting the KNIME processing unit approach ("nodes"), whereas
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Galaxy reflects the perspective of a platform centered around non-developer users interacting with a graphical interface.
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### Parameters description
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### Data/parameter types
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The typing system for parameters in CTD itself is simpler than the other two, providing mainly support for simple types and input/output files, but excluding arrays/lists and complex types. Galaxy adds GUI specific features (`select`, `drill_down`), domain specific features (`color`, `genome_build`, `data_column`), configuration of web services (`base_url`), and tighter integration with workbench internal data management (`library_data`).
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### Command line generation
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All of the specifications include a flexible set of possibilities for the generation of command lines, reflecting the effective heterogeneity of the bioinformatics tools ecosystem ;)
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## Comparison table
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### Tool level
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|Galaxy information |Optional |CTD information |Optional |CWL information |Optional |
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|---|---|---|---|---|---|
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|*description* |X |description |X |label |X |
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|*help* |X |*manual* |X |*doc* |X |
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|*citation* |X |*citation* (for the underlying tool, DOI or doc URL) |X |*SoftwareRequirement.name.specs* (URI) |X |
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| | |*ExecutableName* (overrides the name attribute) |X |*SoftwareRequirement.name.baseCommand[0]* |X |
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| | |*ExecutablePath* (specific path to the executable) |X | | |
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|*command*+*argument* under parameter | |*CLItype* list of input commands with elements mapping |X | *arguments* and/or *inputBindings* |X |
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| | |*logs* (retrospective on execution information - if so probably out of scope)|X | | |
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|*tool/outputs/data/@from_work_dir* (name of file to consume) |X |*relocators* (list of parameters, path pairs)|X |*outputBinding* |X |
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|*@version* (version of wrapper) |X |*@version* (apprarently version of the tool itself)| |*SoftwareRequirements.name.version* (list of known compatible versions of the underlying tool |X |
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|*@name* (just an identifier, not used to build the command itself)||*@name* (also used to build the command itself, unlesss *ExecutableName* is provided)| |baseCommand[0]|X|
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|often part of the *help* text|X|*docURL* (URL to documentation)||||
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|*edam_topics* and *edam_operations* - categories are external to tool definition, in per-server config (toolconf.xml)|X|*category* (any string)|X|can use EDAM or other 3rd party annotation or derive via identifier from external registry or datatype|
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|(often part of help text)|X|*tags*|X|||
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### Parameter level
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**Important remark** The structure of the CTD file is slightly different, because it explicitely allows the definition of "sub-tools" through a nested structure of NODE/ITEM elements. A node is a subgroup of parameters, and ITEM is a parameter.
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Therefore, to focus on Parameter-level information, we consider only the ITEM element here for parameter description in CTD.
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|Galaxy information |Optional |CTD information |Optional |CWL information |Optional |
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|---|---|---|---|---|---|
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| *param* or *data* | | *ITEM* | | *inputs[n]* or *outputs[n]* | |
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|*@name*||*@name*||key of *inp|uts* or *outputs* entry||
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|*@type*||*@type* (Defines the possible types available in the type attribute of ITEM and ITEMLIST.)||type||
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‎cwltool/schemas/v1.0/CommandLineTool.yml

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- {$include: intro.md}
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- |
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## Introduction to v1.0
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## Introduction to CWL Command Line Tool standard v1.0
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This specification represents the first full release from the CWL group.
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Since draft-3, version 1.0 introduces the following changes and additions:
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Since draft-3, version 1.0 introduces the following changes and additions
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to the CWL Command Line Tool standard:
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* The [Directory](#Directory) type.
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* Syntax simplifcations: denoted by the `map<>` syntax. Example: inputs

‎cwltool/schemas/v1.0/Process.yml

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- name: default
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type: Any?
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jsonldPredicate: "cwl:default"
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jsonldPredicate:
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_id: cwl:default
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noLinkCheck: true
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doc: |
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The default value for this parameter if not provided in the input
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object.

‎cwltool/schemas/v1.0/Workflow.yml

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- |
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## Introduction to v1.0
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## Introduction to CWL Workflow standard v1.0
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This specification represents the first full release from the CWL group.
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Since draft-3, this draft introduces the following changes and additions:
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Since draft-3, this draft introduces the following changes and additions
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to the CWL Workflow standard:
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* The `inputs` and `outputs` fields have been renamed `in` and `out`.
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* Syntax simplifcations: denoted by the `map<>` syntax. Example: `in`
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The default value for this parameter if there is no `source`
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field.
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jsonldPredicate: "cwl:default"
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jsonldPredicate:
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_id: "cwl:default"
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noLinkCheck: true
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- name: valueFrom
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type:
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- "null"

‎cwltool/schemas/v1.0/conformance_test_v1.0.yaml

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size: 15
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tool: v1.0/imported-hint.cwl
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doc: Test hints with $import
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- output: {}
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job: v1.0/default_path_job.yml
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tool: v1.0/default_path.cwl
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doc: Test warning instead of error when default path is not found
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- output:
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args: [-A,'2',-B,baz,-C,'10','9','8','7','6','5','4','3','2','1']
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job: v1.0/empty.json
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tool: v1.0/inline-js.cwl
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doc: Test InlineJavascriptRequirement with multiple expressions in the same tool

‎cwltool/schemas/v1.0/v1.0/default_path.cwl

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cwlVersion: v1.0
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class: CommandLineTool
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inputs:
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- id: "file1"
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type: File
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default:
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class: File
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path: default.txt
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outputs: []
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arguments: [cat,$(inputs.file1.path)]

‎cwltool/schemas/v1.0/v1.0/default_path_job.yml

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file1:
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class: File
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path: hello.txt

‎cwltool/schemas/v1.0/v1.0/inline-js.cwl

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cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: echo
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requirements:
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- class: InlineJavascriptRequirement
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inputs:
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- id: args.py
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type: File
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default:
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class: File
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location: args.py
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inputBinding:
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position: -1
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outputs:
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- id: args
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type:
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type: array
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items: string
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baseCommand: python
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arguments:
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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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}

‎cwltool/schemas/v1.1.0-dev1/Process.yml

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jsonldPredicate: "cwl:default"
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jsonldPredicate:
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_id: cwl:default
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‎cwltool/schemas/v1.1.0-dev1/Workflow.yml

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The default value for this parameter if there is no `source`
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jsonldPredicate: "cwl:default"
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jsonldPredicate:
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_id: "cwl:default"
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noLinkCheck: true
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‎cwltool/schemas/v1.1.0-dev1/conformance_test_v1.1.0-dev1.yaml

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tool: v1.1.0-dev1/imported-hint.cwl
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doc: Test hints with $import
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- output: {}
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job: v1.0/default_path_job.yml
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tool: v1.0/default_path.cwl
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doc: Test warning instead of error when default path is not found

‎cwltool/schemas/v1.1.0-dev1/v1.1.0-dev1/default_path.cwl

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cwlVersion: v1.0
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class: CommandLineTool
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inputs:
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- id: "file1"
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type: File
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default:
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class: File
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path: default.txt
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outputs: []
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arguments: [cat,$(inputs.file1.path)]

‎cwltool/schemas/v1.1.0-dev1/v1.1.0-dev1/default_path_job.yml

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file1:
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class: File
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path: hello.txt

‎tests/test_default_path.py

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import unittest
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from cwltool.load_tool import fetch_document, validate_document
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from .util import get_data
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from schema_salad.ref_resolver import Loader
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class TestDefaultPath(unittest.TestCase):
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# Testing that error is not raised when default path is not present
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def test_default_path(self):
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document_loader, workflowobj, uri = fetch_document(
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get_data("tests/wf/default_path.cwl"))
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document_loader, avsc_names, processobj, metadata, uri = validate_document(
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document_loader, workflowobj, uri)
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self.assertIsInstance(document_loader,Loader)
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self.assertIn("cwlVersion",processobj)

‎tests/wf/default_path.cwl

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cwlVersion: v1.0
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class: CommandLineTool
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inputs:
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- id: "file1"
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type: File
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default:
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class: File
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path: default.txt
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outputs: []
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arguments: [cat, $(inputs.file1.path)]
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