name: hmmcopy_mapcounter
description: mapCounter function from HMMcopy utilities, used to generate mappability in non-overlapping windows from a bigwig file
keywords:
  - hmmcopy
  - mapcounter
  - cnv
tools:
  - hmmcopy:
      description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
      homepage: https://github.com/shahcompbio/hmmcopy_utils
      documentation: https://github.com/shahcompbio/hmmcopy_utils
      tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils
      doi: ""
      licence: ["GPL v3"]

input:
  - bigwig:
      type: file
      description: BigWig file with the mappability score of the genome, for instance made with generateMap function.
      pattern: "*.wig"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

  - wig:
      type: file
      description: wig file containing mappability of each window of the genome
      pattern: "*.map.wig"

authors:
  - "@sppearce"