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Merge pull request #229 from common-workflow-language/fix-package-errror
Fix package errror
2 parents 5fd7abd + bb967af commit 5ab452e

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lines changed

‎cwltool/expression.py

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@@ -19,6 +19,7 @@ def jshead(engineConfig, rootvars):
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# type: (List[Text], Dict[Text, Any]) -> Text
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return u"\n".join(engineConfig + [u"var %s = %s;" % (k, json.dumps(v, indent=4)) for k, v in rootvars.items()])
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seg_symbol = r"""\w+"""
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seg_single = r"""\['([^']|\\')+'\]"""
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seg_double = r"""\["([^"]|\\")+"\]"""

‎cwltool/main.py

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@@ -756,5 +756,6 @@ def locToPath(p):
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_logger.removeHandler(stderr_handler)
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_logger.addHandler(defaultStreamHandler)
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if __name__ == "__main__":
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sys.exit(main(sys.argv[1:]))

‎cwltool/pack.py

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@@ -35,8 +35,6 @@ def replace_refs(d, rewrite, stem, newstem):
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else:
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replace_refs(v, rewrite, stem, newstem)
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elif isinstance(d, dict):
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if "package" in d:
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raise Exception("where the fuck did this come from %s" % json.dumps(d, indent=4))
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if "run" in d and isinstance(d["run"], (str, unicode)):
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d["run"] = rewrite[d["run"]]
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for s,v in d.items():
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v = rewrite[r]
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dc = cast(Dict[Text, Any], copy.deepcopy(document_loader.idx[r]))
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dc["id"] = v
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for n in ("name", "package", "cwlVersion"):
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for n in ("name", "cwlVersion"):
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if n in dc:
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del dc[n]
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replace_refs(dc, rewrite, r+"/" if "#" in r else r+"#", v+"/")

‎cwltool/process.py

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@@ -592,6 +592,7 @@ def empty_subtree(dirpath): # type: (Text) -> bool
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raise
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return True
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_names = set() # type: Set[Text]
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‎cwltool/sandboxjs.py

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class JavascriptException(Exception):
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pass
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_logger = logging.getLogger("cwltool")
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JSON = Union[Dict[Text,Any], List[Any], Text, int, long, float, bool, None]

‎cwltool/schemas/README.md

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@@ -40,16 +40,18 @@ Please cite https://dx.doi.org/10.6084/m9.figshare.3115156.v2
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## Implementations
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|Software|Description|CWL support|Platform support|Maturity|
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|Software|Description|CWL support|Platform support|Platform Maturity|
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|--------|-----------|-----------|--------|--------|
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|[cwltool](https://github.com/common-workflow-language/cwltool)|Reference implementation of CWL|[![Build Status](https://ci.commonwl.org/job/cwltool-conformance/badge/icon)](http://ci.commonwl.org/job/cwltool-conformance/lastBuild/testReport/)|Linux, OS X, local execution only|Production|
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|[Arvados](https://arvados.org)|Distributed computing platform for data analysis on massive data sets. [Using CWL on Arvados](http://doc.arvados.org/user/cwl/cwl-runner.html)|[![Build Status](https://ci.commonwl.org/job/arvados-conformance/badge/icon)](http://ci.commonwl.org/job/arvados-conformance/lastBuild/testReport/)|AWS, GCP, Azure, Slurm|Production|
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|[Toil](https://github.com/BD2KGenomics/toil)|Toil is a workflow engine entirely written in Python.|[![Build Status](https://ci.commonwl.org/job/toil-conformance/badge/icon)](http://ci.commonwl.org/job/toil-conformance/lastBuild/testReport/)|AWS, GCP, Azure, OpenStack, Grid Engine, Mesos|Production|
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|[Rabix Bunny](https://github.com/rabix/bunny)|Reproducible Analyses for Bioinformatics|[![Build Status](https://ci.commonwl.org/buildStatus/icon?job=rabix-conformance)](https://ci.commonwl.org/job/rabix-conformance/)|Java|alpha|
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|[Apache Taverna](http://taverna.incubator.apache.org/)|Domain-independent Workflow Management System|[alpha](https://issues.apache.org/jira/browse/TAVERNA-900)|Java|Production|
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|[Galaxy](https://galaxyproject.org/)|Web-based platform for data intensive biomedical research.|[alpha](https://github.com/common-workflow-language/galaxy)|Python|Production|
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|[AWE](https://github.com/MG-RAST/AWE)|Workflow and resource management system for bioinformatics data analysis.|[alpha](https://github.com/wgerlach/AWE)|Go|Production|
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|[Funnel](https://github.com/bmeg/funnel)|Use Google Genomics Pipeline API with CWL|alpha|GCP|alpha|
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|[Rabix Bunny](https://github.com/rabix/bunny)|Reproducible Analyses for Bioinformatics|alpha|Java|alpha|
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|[xenon-cwl-runner](https://github.com/NLeSC/xenon-cwl-runner)|Run CWL workflows using Xenon|alpha|[any Xenon backend](http://nlesc.github.io/Xenon/): local, ssh, SLURM, Torque, Grid Engine|Production|
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## Repositories of CWL Tools and Workflows
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@@ -64,10 +66,12 @@ Please cite https://dx.doi.org/10.6084/m9.figshare.3115156.v2
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|--------|-----------|
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|[cwltest](https://github.com/common-workflow-language/cwltest)|CWL testing framework, automated testing of tools and workflows written with CWL|
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|[cwl-upgrader](https://github.com/common-workflow-language/cwl-upgrader)|Upgrade CWL documents from draft-3 to v1.0|
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|[argparse2cwl](https://github.com/common-workflow-language/gxargparse#argparse2cwl)|Generate CWL CommandLineTool wrapper from Python programs that use argparse. Also supports [click](http://click.pocoo.org/5/) argument parser.|
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|[argparse2tool](https://github.com/erasche/argparse2tool#cwl-specific-functionality)|Generate CWL CommandLineTool wrappers (and/or Galaxy tool descriptions) from Python programs that use argparse. Also supports the [click](http://click.pocoo.org/5/) argument parser.|
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|[cwl2argparse](https://github.com/common-workflow-language/cwl2argparse)|Generate Python argparse code from CWL CommandLineTool description.|
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|[pypi2cwl](https://github.com/common-workflow-language/pypi2cwl)|Automatically run argparse2cwl on any package in PyPi|
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|[cwlavro](https://github.com/common-workflow-language/cwlavro)|Java classes for loading CWL documents|
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|[acd2cwl](https://github.com/common-workflow-language/acd2cwl)|CWL generator for ACD (EMBOSS) files |
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|[CWLviewer](https://github.com/MarkRobbo/CWLViewer)|A web application to view and share Common Workflow Language workflows|
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## Support, Community and Contributing
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‎cwltool/schemas/draft-2/draft-2/binding-test.cwl

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inputBinding:
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position: -1
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outputs: []
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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: ["bwa", "mem"]

‎cwltool/schemas/draft-2/draft-2/cat1-testcli.cwl

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}
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},
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{
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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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path: args.py
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},
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inputBinding: {
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position: -1
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}
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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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"path": "args.py"
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},
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"inputBinding": {
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"position": -1
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}
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}
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],
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"outputs": [],
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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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}
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}],
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"baseCommand": "python",
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"arguments": ["cat"]
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}

‎cwltool/schemas/draft-2/draft-2/tmap-tool.cwl

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}
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},
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{
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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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path: args.py
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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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"path": "args.py"
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},
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inputBinding: {
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position: -1
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"inputBinding": {
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"position": -1
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}
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}
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],
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"glob": "output.sam"
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},
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"type": ["null", "File"]
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},
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{
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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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}
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}
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],
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"requirements": [

‎cwltool/schemas/draft-3/draft-3/binding-test.cwl

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inputBinding:
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outputs: []
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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: ["bwa", "mem"]

‎cwltool/schemas/draft-3/draft-3/cat1-testcli.cwl

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}
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},
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{
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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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path: args.py
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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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"path": "args.py"
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},
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inputBinding: {
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position: -1
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"inputBinding": {
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"position": -1
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}
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}
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],
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"outputs": [],
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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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}
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}],
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"baseCommand": "python",
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"arguments": ["cat"]
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}

‎cwltool/schemas/draft-3/draft-3/tmap-tool.cwl

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}
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},
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{
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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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path: args.py
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},
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inputBinding: {
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}
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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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"path": "args.py"
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},
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"inputBinding": {
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"position": -1
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}
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}
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],
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"outputs": [
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"glob": "output.sam"
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},
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"type": ["null", "File"]
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},
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{
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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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}
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}
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],
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"requirements": [

‎cwltool/schemas/v1.0/CommandLineTool.yml

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- name: package
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type: string
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doc: "The common name of the software to be configured."
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jsonldPredicate: "@id"
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- name: version
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type: string[]?
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doc: "The (optional) version of the software to configured."

‎cwltool/schemas/v1.0/UserGuide.yml

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- |
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## Parameter references
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In a previous example, we used extracted a file using the "tar" program.
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However, that example was very limited becuase it assumed that the file
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In a previous example, we extracted a file using the "tar" program.
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However, that example was very limited because it assumed that the file
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we were interested in was called "hello.txt". In this example, you will
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see how to reference the value of input parameters dynamically from other
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fields.

‎cwltool/schemas/v1.0/concepts.md

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[Semantic Annotations for Linked Avro Data (SALAD) Specification](SchemaSalad.html).
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An implementation may formally validate the structure of a CWL document using
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SALAD schemas located at
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https://github.com/common-workflow-language/common-workflow-language/tree/master/draft-4
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https://github.com/common-workflow-language/common-workflow-language/tree/master/v1.0
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## Identifiers
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