name: "motus_merge"
description: Taxonomic meta-omics profiling using universal marker genes
keywords:
  - classify
  - metagenomics
  - fastq
  - taxonomic profiling
  - merging
  - merge
  - otu table
tools:
  - "motus":
      description: "Marker gene-based OTU (mOTU) profiling"
      homepage: "https://motu-tool.org/"
      documentation: "https://github.com/motu-tool/mOTUs/wiki"
      tool_dev_url: "https://github.com/motu-tool/mOTUs"
      doi: "10.1038/s41467-019-08844-4"
      licence: "['GPL v3']"

input:
  - input:
      type: file
      description: |
        List of output files (more than one) from motus profile,
        or a single directory containing motus output files.
  - db:
      type: directory
      description: |
        mOTUs database downloaded by `motus downloadDB`
        pattern: "db_mOTU/"
  - profile_version_yml:
      type: file
      description: |
        A single versions.yml file output from motus/profile. motus/merge cannot reconstruct
        this itself without having the motus database present and configured with the tool
        so here we take it from what is already reported by the upstream module.
      pattern: "versions.yml"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - txt:
      type: file
      description: OTU table in txt format, if BIOM format not requested
      pattern: "*.txt"
  - biom:
      type: file
      description: OTU table in biom format, if BIOM format requested
      pattern: "*.biom"

authors:
  - "@jfy133"