name: maltextract
description: Tool for evaluation of MALT results for true positives of ancient metagenomic taxonomic screening
keywords:
  - malt
  - MaltExtract
  - HOPS
  - alignment
  - metagenomics
  - ancient DNA
  - aDNA
  - palaeogenomics
  - archaeogenomics
  - microbiome
  - authentication
  - damage
  - edit distance
tools:
  - maltextract:
      description: Java tool to work with ancient metagenomics
      homepage: https://github.com/rhuebler/hops
      documentation: https://github.com/rhuebler/hops
      tool_dev_url: https://github.com/rhuebler/hops
      doi: "https://doi.org/10.1186/s13059-019-1903-0"
      licence: ["GPL 3"]

input:
  - rma6:
      type: file
      description: RMA6 files from MALT
      pattern: "*.rma6"
  - taxon_list:
      type: file
      description: List of target taxa to evaluate
      pattern: "*.txt"
  - ncbi_dir:
      type: directory
      description: Directory containing NCBI taxonomy map and tre files
      pattern: "${ncbi_dir}/"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - results:
      type: directory
      description: Directory containing MaltExtract text results files
      pattern: "*.rma6"

authors:
  - "@jfy133"