name: mtnucratio
description: A small Java tool to calculate ratios between MT and nuclear sequencing reads in a given BAM file.
keywords:
  - mtnucratio
  - ratio
  - reads
  - bam
  - mitochondrial to nuclear ratio
  - mitochondria
  - statistics
tools:
  - mtnucratio:
      description: A small tool to determine MT to Nuclear ratios for NGS data.
      homepage: https://github.com/apeltzer/MTNucRatioCalculator
      documentation: https://github.com/apeltzer/MTNucRatioCalculator
      tool_dev_url: https://github.com/apeltzer/MTNucRatioCalculator
      doi: "10.1186/s13059-016-0918-z"
      licence: ['GPL v3']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: (coordinate) sorted BAM/SAM file
      pattern: "*.{bam,sam}"
  - mt_id:
      type: string
      description: Identifier of the contig/chromosome of interest (e.g. chromosome, contig) as in the aligned against reference FASTA file, e.g. mt or chrMT for mitochondria

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"
  - mtnucratio:
      type: file
      description: Text file containing metrics (mtreads, mt_cov_avg, nucreads, nuc_cov_avg, mt_nuc_ratio)
      pattern: "*.mtnucratio"
  - json:
      type: file
      description: JSON file, containing metadata map with sample name, tool name and version, and metrics as in txt file
      pattern: "*.json"

authors:
  - "@louperelo"