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: - versions: type: file description: File containing software versions pattern: "versions.yml" - 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"