name: "atlas_pmd"
description: Estimate the post-mortem damage patterns of DNA
keywords:
  - ancient DNA
  - post mortem damage
  - bam
tools:
  - "atlas":
      description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity"
      homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
      documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
      tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
      doi: "10.1101/105346"
      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]

  - bam:
      type: file
      description: Single input BAM file
      pattern: "*.bam"
  - bai:
      type: file
      description: The BAI file for the input BAM file
      pattern: "*.bai"
  - fasta:
      type: file
      description: The reference genome provided as FASTA file
      pattern: "*.fasta"
  - fai:
      type: file
      description: The FAI file for the reference genome FASTA file
      pattern: "*.fai"
  - pool_rg_txt:
      type: file
      description: |
        Optional. Provide the names of read groups that should be merged for PMD estimation.
        All read groups that should be pooled listed on one line, separated by any white space.
        Other read groups will be recalibrated separately.
      pattern: "*.txt"

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"

  - empiric:
      type: file
      description: A list of pmd patterns estimated with the empirical method for each readgroup
      pattern: "*_PMD_input_Empiric.txt"
  - exponential:
      type: file
      description: A list of pmd patterns estimated with the exponential method for each readgroup
      pattern: "*_PMD_input_Exponential.txt"
  - counts:
      type: file
      description: |
        The counts of all possible transitions for each read position
        (or up to a certain position, see specific command length)
      pattern: "*_PMD_Table_counts.txt"
  - table:
      type: file
      description: |
        For all possible transitions the ratio of the transition counts,
        which are taken from the _counts.txt table, over the total amount
        of the base that was mutated, for each position and readgroup
      pattern: "*_PMD_Table.txt"

authors:
  - "@maxibor"
  - "@merszym"