Dockstore.cwl

#!/usr/bin/env cwl-runner

class: CommandLineTool

cwlVersion: v1.0

dct:contributor:
  foaf:name: Andy Yang
  foaf:mbox: mailto:ayang@oicr.on.ca
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'
requirements:
- class: DockerRequirement
  dockerPull: quay.io/cancercollaboratory/dockstore-tool-samtools-index:1.0
- class: InlineJavascriptRequirement
  expressionLib:
  - var new_ext = function() { var ext=inputs.bai?'.bai':inputs.csi?'.csi':'.bai';
    return inputs.input.path.split('/').slice(-1)[0]+ext; };
inputs:
  input:
    type: File
    inputBinding:
      position: 2

    doc: |
      Input bam file.
  interval:
    type: int?
    inputBinding:
      position: 1
      prefix: -m
    doc: |
      Set minimum interval size for CSI indices to 2^INT [14]
  csi:
    type: boolean
    default: false
    doc: |
      Generate CSI-format index for BAM files
  bai:
    type: boolean
    default: false
    doc: |
      Generate BAI-format index for BAM files [default]
outputs:
  index:
    type: File
    outputBinding:
      glob: $(new_ext())

    doc: The index file
baseCommand: [samtools, index]
arguments:
- valueFrom: $(inputs.bai?'-b':inputs.csi?'-c':[])
  position: 1
- valueFrom: $(new_ext())
  position: 3 

doc: |
  Prints alignments in the specified input alignment file.

  Usage: samtools index [-bc] [-m INT] <in.bam> aln.bam|aln.cram
  Options:
    -b       Generate BAI-format index for BAM files [default]
    -c       Generate CSI-format index for BAM files
    -m INT   Set minimum interval size for CSI indices to 2^INT [14]

  For a CRAM file aln.cram, index file aln.cram.crai will be created. For a BAM file aln.bam, either aln.bam.bai or aln.bam.csi will be created, depending on the index format selected.