name: amps
description: Post-processing script of the MaltExtract component of the HOPS package
keywords:
  - malt
  - MaltExtract
  - HOPS
  - amps
  - alignment
  - metagenomics
  - ancient DNA
  - aDNA
  - palaeogenomics
  - archaeogenomics
  - microbiome
  - authentication
  - damage
  - edit distance
  - post Post-processing
  - visualisation
tools:
  - amps:
      description: Post-processing script of the MaltExtract tool for ancient metagenomics
      homepage: "https://github.com/rhuebler/HOPS"
      documentation: "https://github.com/keyfm/amps"
      tool_dev_url: "https://github.com/keyfm/amps"
      doi: "10.1186/s13059-019-1903-0"
      licence: ["GPL >=3"]

input:
  - maltextract_results:
      type: directory
      description: MaltExtract output directory
      pattern: "results/"
  - taxon_list:
      type: file
      description: List of target taxa to evaluate used in MaltExtract
      pattern: "*.txt"
  - filter:
      type: string
      description: The filter mode used in MaltExtract
      pattern: "def_anc|default|scan|ancient|crawl"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - json:
      type: file
      description: Candidate summary heatmap in MultiQC compatible JSON format
      pattern: "heatmap_overview_Wevid.json"
  - summary_pdf:
      type: file
      description: Candidate summary heatmap in PDF format
      pattern: "heatmap_overview_Wevid.pdf"
  - tsv:
      type: file
      description: Candidate summary heatmap in TSV format
      pattern: "heatmap_overview_Wevid.tsv"
  - candidate_pdfs:
      type: directory
      description: Directory of per sample output PDFs organised by reference
      pattern: "pdf_candidate_profiles/"

authors:
  - "@jfy133"