name: deeptools_computematrix
description: calculates scores per genome regions for other deeptools plotting utilities
keywords:
  - genome
  - regions
  - scores
  - matrix
tools:
  - deeptools:
      description: A set of user-friendly tools for normalization and visualization of deep-sequencing data
      documentation: https://deeptools.readthedocs.io/en/develop/index.html
      tool_dev_url: https://github.com/deeptools/deepTools
      doi: "10.1093/nar/gku365"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - bigwig:
      type: file
      description: bigwig file containing genomic scores
      pattern: "*.{bw,bigwig}"
  - bed:
      type: file
      description: bed file containing genomic regions
      pattern: "*.{bed}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - matrix:
      type: file
      description: |
        gzipped matrix file needed by the plotHeatmap and plotProfile
        deeptools utilities
      pattern: "*.{computeMatrix.mat.gz}"
  - table:
      type: file
      description: |
        tabular file containing the scores of the generated matrix
      pattern: "*.{computeMatrix.vals.mat.tab}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@jeremy1805"
  - "@emiller88"
  - "@drpatelh"
  - "@joseespinosa"
