name: cooler_cload
description: Create a cooler from genomic pairs and bins
keywords:
  - cool
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 ]
  - pairs:
      type: file
      description: Path to contacts (i.e. read pairs) file.
  - index:
      type: file
      description: Path to index file of the contacts.
  - cool_bin:
      type: value
      description: Bins size in bp
  - chromsizes:
      type: file
      description: Path to a chromsizes file.

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "versions.yml"
  - cool:
      type: file
      description: Output COOL file path
      pattern: "*.cool"
  - cool_bin:
      type: value
      description: Bins size in bp

authors:
  - "@jianhong"