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9dceffce2f
* Add the language for the Common Workflow Language standards * add CWL grammer * add MIT licensed CWL sample * script/set-language-ids --update for CWL
37 lines
944 B
Plaintext
37 lines
944 B
Plaintext
#!/usr/bin/env cwl-runner
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# Originally from
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# https://github.com/Duke-GCB/GGR-cwl/blob/54e897263a702ff1074c8ac814b4bf7205d140dd/utils/trunk-peak-score.cwl
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# Released under the MIT License:
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# https://github.com/Duke-GCB/GGR-cwl/blob/54e897263a702ff1074c8ac814b4bf7205d140dd/LICENSE
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# Converted to CWL v1.0 syntax using
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# https://github.com/common-workflow-language/cwl-upgrader
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# and polished by Michael R. Crusoe <mrc@commonwl.org>
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# All modifications also released under the MIT License
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cwlVersion: v1.0
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class: CommandLineTool
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doc: Trunk scores in ENCODE bed6+4 files
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hints:
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DockerRequirement:
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dockerPull: dukegcb/workflow-utils
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inputs:
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peaks:
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type: File
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sep:
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type: string
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default: \t
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outputs:
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trunked_scores_peaks:
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type: stdout
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baseCommand: awk
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arguments:
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- -F $(inputs.sep)
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- BEGIN{OFS=FS}$5>1000{$5=1000}{print}
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- $(inputs.peaks.path)
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stdout: $(inputs.peaks.nameroot).trunked_scores$(inputs.peaks.nameext)
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