name: cnvpytor_view
description: view function to generate vcfs
keywords:
  - cnv calling
tools:
  - cnvpytor:
      description: calling CNVs using read depth
      homepage: https://github.com/abyzovlab/CNVpytor
      documentation: https://github.com/abyzovlab/CNVpytor
      tool_dev_url: https://github.com/abyzovlab/CNVpytor
      doi: "10.1101/2021.01.27.428472v1"
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - pytor_files:
      type: file
      description: pytor file containing cnv calls. To merge calls from multiple samples use a list of files.
      pattern: "*.{pytor}"
  - bin_sizes:
      type: string
      description: list of binsizes separated by space e.g. "1000 10000" and "1000"
  - output_format:
      type: string
      description: output format of the cnv calls. Valid entries are "tsv", "vcf", and "xls"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - tsv:
      type: file
      description: tsv file containing cnv calls
      pattern: "*.{tsv}"
  - vcf:
      type: file
      description: vcf file containing cnv calls
      pattern: "*.{vcf}"
  - xls:
      type: file
      description: xls file containing cnv calls
      pattern: "*.{xls}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@sima-r"
  - "@ramprasadn"