name: malt_build
description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.
keywords:
  - malt
  - alignment
  - metagenomics
  - ancient DNA
  - aDNA
  - palaeogenomics
  - archaeogenomics
  - microbiome
  - database
tools:
  - malt:
      description: A tool for mapping metagenomic data
      homepage: https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/malt/
      documentation: https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf
      tool_dev_url: None
      doi: "10.1038/s41559-017-0446-6"
      licence: ["GPL v3"]

input:
  - fastas:
      type: file
      description: Directory of, or list of FASTA reference files for indexing
      pattern: "*/|*.fasta"
  - seq_type:
      type: string
      description: Type of input data
      pattern: "DNA|Protein"
  - mapping_file:
      type: file
      description: An unzipped MEGAN mapping file in .abin format (pre-2020), downloadable from https://software-ab.informatik.uni-tuebingen.de/download/megan6/old.html
      pattern: "*.abin"
  - mapping_type:
      type: value
      description: What type of accession to use for database construction.
      pattern: "gi|ref|syn"
  - mapping_type:
      type: value
      description: Which database the mapping file is derived from.
      pattern: "eggnog|interpro2go|kegg|seed|taxonomy"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - index:
      type: directory
      description: Directory containing MALT database index directory
      pattern: "malt_index/"
  - log:
      type: file
      description: Log file from STD out of malt-build
      pattern: "malt-build.log"

authors:
  - "@jfy133"