├── .gitignore ├── LICENSE.TXT ├── MANIFEST.in ├── README.md ├── argparse ├── __init__.py ├── argparse_cwl_translation.py └── argparse_galaxy_translation.py ├── click ├── __init__.py └── click_cwl_translation.py ├── cmdline2cwl ├── __init__.py ├── cwl_tool.py └── templates │ ├── cwltool.j2 │ ├── cwltool_inputs.j2 │ └── cwltool_outputs.j2 ├── example.py ├── example.xml ├── 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 ├── gxargparse ├── __init__.py └── check_path.py ├── requirements.txt ├── setup.cfg ├── setup.py └── test ├── __init__.py ├── cwl_classes.py ├── test-data ├── index.cwl ├── index.py ├── index_new.cwl ├── inp.txt ├── inp.txt.idx1 ├── job.json ├── main.cwl ├── search.cwl ├── search.py └── search_new.cwl ├── test_arg2cwl.py ├── test_click2cwl.py └── test_utils.py /.gitignore: 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