name: cooler_digest
description: Generate fragment-delimited genomic bins
keywords:
  - digest
  - enzyme
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:
  - fasta:
      type: file
      description: Genome assembly FASTA file or folder containing FASTA files (uncompressed).
      pattern: "*.{fasta,fa}"
  - chromsizes:
      type: file
      description: Path to a chromsizes file.
  - enzyme:
      type: String
      description: Name of restriction enzyme. e.g. CviQI.
      documentation: http://biopython.org/DIST/docs/cookbook/Restriction.html

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - bed:
      type: file
      description: A genome segmentation of restriction fragments as a BED file.
      pattern: "*.{bed}"

authors:
  - "@jianhong"