name: cooler_dump
description: Dump a cooler’s data to a text stream.
keywords:
  - dump
tools:
  - cooler:
      description: Sparse binary format for genomic interaction matrices
      homepage: https://cooler.readthedocs.io/en/latest/index.html
      documentation: https://cooler.readthedocs.io/en/latest/index.html
      tool_dev_url: https://github.com/open2c/cooler
      doi: "10.1093/bioinformatics/btz540"
      licence: ['BSD-3-Clause']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - cool:
      type: file
      description: Path to COOL file
      pattern: "*.{cool,mcool}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - bedpe:
      type: file
      description: Output text file
      pattern: "*.bedpe"

authors:
  - "@jianhong"