name: malt_run
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
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:
  - fastqs:
      type: file
      description: Input FASTQ files
      pattern: "*.{fastq.gz,fq.gz}"
  - mode:
      type: string
      description: Program mode
      pattern: 'Unknown|BlastN|BlastP|BlastX|Classifier'
  - index:
      type: directory
      description: Index/database directory from malt-build
      pattern: '*/'
output:
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
  - rma6:
      type: file
      description: MEGAN6 RMA6 file
      pattern: "*.rma6"
  - sam:
      type: file
      description: Alignment files in Tab, Text or MEGAN-compatible SAM format
      pattern: "*.{tab,txt,sam}"
  - log:
      type: file
      description: Log of verbose MALT stdout
      pattern: "malt-run.log"

authors:
  - "@jfy133"