Dockstore.cwl

#!/usr/bin/env cwl-runner

class: CommandLineTool
id: bedtools-genomecov
label: bedtools-genomecov
cwlVersion: v1.0

dct:creator:
  '@id': http://orcid.org/0000-0001-9102-5681
  foaf:name: Andrey Kartashov
  foaf:mbox: mailto:Andrey.Kartashov@cchmc.org
dct:description: 'Developed at Cincinnati Children’s Hospital Medical Center for the
  CWL consortium http://commonwl.org/ Original URL: https://github.com/common-workflow-language/workflows'
dct:contributor:
  '@id': http://orcid.org/orcid.org/0000-0002-6130-1021
  foaf:name: Denis Yuen
  foaf:mbox: mailto:help@cancercollaboratory.org
requirements:
- class: DockerRequirement
  dockerPull: quay.io/collaboratory/dockstore-tool-bedtools-genomecov:1.0
- class: InlineJavascriptRequirement

inputs:
  genomecoverageout: string
  scale:
    type: float?
    inputBinding:
      position: 4
      prefix: -scale

    doc: |
      Scale the coverage by a constant factor.
      Each coverage value is multiplied by this factor before being reported.
      Useful for normalizing coverage by, e.g., reads per million (RPM).
      - Default is 1.0; i.e., unscaled.
      - (FLOAT)
  max:
    type: int?
    inputBinding:
      position: 4
      prefix: -max
    doc: |
      Combine all positions with a depth >= max into
      a single bin in the histogram. Irrelevant
      for -d and -bedGraph
      - (INTEGER)
  m5:
    type: boolean?
    inputBinding:
      position: 4
      prefix: '-5'
    doc: |
      Calculate coverage of 5" positions (instead of entire interval).
  dept:
    type:
      name: JustDepts
      type: enum
      symbols: [-bg, -bga, -d]
    inputBinding:
      position: 4

  dz:
    type: boolean?
    inputBinding:
      position: 4
      prefix: -dz
    doc: |
      Report the depth at each genome position (with zero-based coordinates).
      Reports only non-zero positions.
      Default behavior is to report a histogram.
  split:
    type: boolean?
    inputBinding:
      position: 4
      prefix: -split
    doc: |
      reat "split" BAM or BED12 entries as distinct BED intervals.
      when computing coverage.
      For BAM files, this uses the CIGAR "N" and "D" operations
      to infer the blocks for computing coverage.
      For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds
      fields (i.e., columns 10,11,12).
  m3:
    type: boolean?
    inputBinding:
      position: 4
      prefix: '-3'
    doc: |
      Calculate coverage of 3" positions (instead of entire interval).
  input:
    type: File
    inputBinding:
      position: 1
      valueFrom: |
        ${
          var prefix = ((/.*\.bam$/i).test(inputs.input.path))?'-ibam':'-i';
          return [prefix,inputs.input.path];
        }
      secondaryFiles: |
        ${
          if ((/.*\.bam$/i).test(inputs.input.path))
             return {"path": inputs.input.path+".bai", "class": "File"};
          return [];
        }


    doc: |
      The input file can be in BAM format
          (Note: BAM _must_ be sorted by position)
      or <bed/gff/vcf>
  strand:
    type: string?
    inputBinding:
      position: 4
      prefix: -strand
    doc: |
      Calculate coverage of intervals from a specific strand.
      With BED files, requires at least 6 columns (strand is column 6).
      - (STRING): can be + or -
  genomeFile:
    type: File
    inputBinding:
      position: 2
      prefix: -g
    doc: Input genome file.
outputs:
  genomecoverage:
    type: File
    outputBinding:
      glob: $(inputs.genomecoverageout)

    doc: The file containing the genome coverage
stdout: $(inputs.genomecoverageout)

baseCommand: [bedtools, genomecov]
doc: |
  Tool:    bedtools genomecov (aka genomeCoverageBed)
  Sources: https://github.com/arq5x/bedtools2
  Summary: Compute the coverage of a feature file among a genome.
  Usage: bedtools genomecov [OPTIONS] -i <bed/gff/vcf> -g <genome>