bamscale-cov.cwl

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool

label: BAMscale-cov
doc: Calculate coverage of BED coordinates in BAM file(s)

requirements:
  InlineJavascriptRequirement: {}

hints:
  - $import: bamscale.yml

inputs:
  l:
    type: string?
    inputBinding:
      position: 1
      prefix: -l
    doc: |
      Sequencing type to be used. Can be: single, paired, and auto (default: autodetect)
  f:
    type: string?
    inputBinding:
      position: 1
      prefix: -f
    doc: |
      Compute coverage using fragments instead of reads (default: no)
  s:
    type: string?
    inputBinding:
      position: 1
      prefix: -s
    doc: |
      Reads need to have same orientation of peaks (default: unstranded)
  r:
    type: string?
    inputBinding:
      position: 1
      prefix: -r
    doc: |
      Reads need to have reverse orientation of peaks (default: unstranded)
  e:
    type: int?
    inputBinding:
      position: 2
      prefix: -e
    doc: |
      Compute sequencing coverage from BAM file quickly using the index (option '0'),
      or count number of reads by parsing entire BAM file (slower, but more accurate; set to '1' [default])
  c:
    type: File?
    inputBinding:
      position: 2
      prefix: -c
    doc: |
      Input file with list of chromosomes to blacklist when computing coverage for normalization
  u:
    type: int?
    inputBinding:
      position: 2
      prefix: -u
    doc: |
      BED file with regions to subtract when computing coverage for normalization
      These coordinates should not overlap so reads are not counted multiple times
  q:
    type: int?
    inputBinding:
      position: 3
      prefix: -q
    doc: |
      Minimum (at least) mapping quality (default: 0)
  d:
    type: string?
    inputBinding:
      position: 3
      prefix: -d
    doc: |
      Keep duplicated reads (default: no)
  p:
    type: string?
    inputBinding:
      position: 3
      prefix: -p
    doc: |
      Do not filter un-proper alignments (default: filter)
  m:
    type: string?
    inputBinding:
      position: 3
      prefix: -m
    doc: |
      Do not remove reads with unmapped pairs
  g:
    type: int?
    inputBinding:
      position: 3
      prefix: -g
    doc: |
      Minimum fragment size for read pairs (default: 0)
  x:
    type: int?
    inputBinding:
      position: 3
      prefix: -x
    doc: |
      Maximum fragment size for read pairs (default: 2000)
  w:
    type: int?
    inputBinding:
      position: 3
      prefix: -w
    doc: |
      Filter reads based on fragment size (default: no)
  t:
    type: int?
    inputBinding:
      position: 4
      prefix: -t
    doc: |
      No. of threads to use (default: 1)
  n:
    type: string
    inputBinding:
      position: 4
      prefix: -n
    doc: |
      Output prefix for file names (default: none)
  bed:
    type: File
    inputBinding:
      position: 5
      prefix: --bed
    doc: |
      Input BED file
  bam:
    type:
      type: array
      items: File
      inputBinding:
        prefix: --bam
        separate: true
    secondaryFiles: .bai
    inputBinding:
      position: 6
    doc: |
      Input BAM file. This can be specified multiple times in case of multiple BAM files

outputs:
  output:
    type: File[]
    outputBinding:
      glob: $(inputs.n)*

baseCommand: ["BAMscale", "cov"]

s:author:
  - class: s:Person
    s:identifier: https://orcid.org/0000-0002-4108-5982
    s:email: mailto:r78v10a07@gmail.com
    s:name: Roberto Vera Alvarez

s:codeRepository: https://github.com/ncbi/BAMscale
s:license: https://spdx.org/licenses/OPL-1.0

$namespaces:
  s: http://schema.org/

$schemas:
  - http://schema.org/docs/schema_org_rdfa.html