name: "endorspy"
description: endorS.py calculates endogenous DNA from samtools flagstat files and print to screen
keywords:
  - endogenous DNA
  - ancient DNA
  - percent on target
  - statistics
tools:
  - "endorspy":
      description: "endorS.py calculates endogenous DNA from samtools flagstat files and print to screen"
      homepage: "https://github.com/aidaanva/endorS.py"
      documentation: "https://github.com/aidaanva/endorS.py"
      tool_dev_url: "https://github.com/aidaanva/endorS.py"
      doi: "10.7717/peerj.10947"
      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - stats:
      type: file
      description: output of samtools flagstat in a text file
  - stats_optional:
      type: file
      description: output of a second samtools flagstat run in a text file. If two files are supplied,
        the mapped reads of the second file is divided by the total reads in the first, since it
        assumes that the <samplefile.stats> are related to the same sample. Useful after BAM filtering.

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"
  - json:
      type: file
      description: file with the endogenous DNA calculation tailored for multiQC
      pattern: "*_mqc.json"

authors:
  - "@aidaanva"