name: "phantompeakqualtools"

description:
keywords:
  - "ChIP-Seq"
  - "QC"
  - "phantom peaks"
tools:
  - "phantompeakqualtools":
      description: |
        "This package computes informative enrichment and quality measures
        for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used
        to obtain robust estimates of the predominant fragment length or
        characteristic tag shift values in these assays."
      homepage: "None"
      documentation: "https://github.com/kundajelab/phantompeakqualtools"
      tool_dev_url: "https://github.com/kundajelab/phantompeakqualtools"
      doi: "https://doi.org/10.1101/gr.136184.111"
      licence: "['BSD-3-clause']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"

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"
  - spp:
      type: file
      description: |
        A ChIP-Seq Processing Pipeline file containing
        peakshift/phantomPeak results
      pattern: "*.{out}"
  - pdf:
      type: file
      description: A pdf containing save cross-correlation plots
      pattern: "*.{pdf}"
  - rdata:
      type: file
      description: Rdata file containing the R session
      pattern: "*.{Rdata}"

authors:
  - "@drpatelh"
  - "@Emiller88"
  - "@JoseEspinosa"