├── .github └── workflows │ ├── ci.yml │ └── publish.yml ├── .gitignore ├── .travis.yml ├── LICENSE.TXT ├── MANIFEST.in ├── README.rst ├── argparse2tool ├── __init__.py ├── check_path.py ├── cmdline2cwl │ ├── __init__.py │ ├── cwl_tool.py │ └── templates │ │ ├── cwltool.j2 │ │ ├── cwltool_inputs.j2 │ │ └── cwltool_outputs.j2 ├── cmdline2gxml │ └── __init__.py └── dropins │ ├── argparse │ ├── __init__.py │ ├── argparse_cwl_translation.py │ └── argparse_galaxy_translation.py │ └── click │ ├── __init__.py │ └── click_cwl_translation.py ├── examples ├── argparse │ └── cnvkit-tools │ │ ├── check_wrappers_in_dir.sh │ │ ├── cnvkit-access.cwl │ │ ├── cnvkit-antitarget.cwl │ │ ├── cnvkit-batch.cwl │ │ ├── cnvkit-breaks.cwl │ │ ├── cnvkit-call.cwl │ │ ├── cnvkit-coverage.cwl │ │ ├── cnvkit-diagram.cwl │ │ ├── cnvkit-export-bed.cwl │ │ ├── cnvkit-export-cdt.cwl │ │ ├── cnvkit-export-jtv.cwl │ │ ├── cnvkit-export-nexus-basic.cwl │ │ ├── cnvkit-export-nexus-ogt.cwl │ │ ├── cnvkit-export-seg.cwl │ │ ├── cnvkit-export-theta.cwl │ │ ├── cnvkit-export-vcf.cwl │ │ ├── cnvkit-fix.cwl │ │ ├── cnvkit-gainloss.cwl │ │ ├── cnvkit-gender.cwl │ │ ├── cnvkit-heatmap.cwl │ │ ├── cnvkit-import-picard.cwl │ │ ├── cnvkit-import-seg.cwl │ │ ├── cnvkit-import-theta.cwl │ │ ├── cnvkit-loh.cwl │ │ ├── cnvkit-metrics.cwl │ │ ├── cnvkit-reference.cwl │ │ ├── cnvkit-rescale.cwl │ │ ├── cnvkit-scatter.cwl │ │ ├── cnvkit-segment.cwl │ │ ├── cnvkit-segmetrics.cwl │ │ ├── cnvkit-target.cwl │ │ ├── cnvkit-version.cwl │ │ ├── data.json │ │ ├── genome2access.cwl │ │ ├── genome2access.py │ │ └── output.txt ├── click │ └── genmod-tools │ │ ├── genmod-annotate.cwl │ │ ├── genmod-build.cwl │ │ ├── genmod-compound.cwl │ │ ├── genmod-filter.cwl │ │ ├── genmod-models.cwl │ │ ├── genmod-score.cwl │ │ └── genmod-sort.cwl ├── example-click.cwl ├── example-click.py ├── example-sub-bar.xml ├── example-sub-foo.xml ├── example-sub.cwl ├── example-sub.py ├── example-sub.xml ├── example.cwl ├── example.py └── example.xml ├── 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