name: "megan_rma2info"
description: Analyses an RMA file and exports information in text format
keywords:
  - megan
  - rma6
  - classification
  - conversion
tools:
  - "megan":
      description: "A tool for studying the taxonomic content of a set of DNA reads"
      homepage: "https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/"
      documentation: "https://software-ab.informatik.uni-tuebingen.de/download/megan6/welcome.html"
      tool_dev_url: "https://github.com/husonlab/megan-ce"
      doi: "10.1371/journal.pcbi.1004957"
      licence: "['GPL >=3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - rma6:
      type: file
      description: RMA6 file from MEGAN or MALT
      pattern: "*.rma6"
  - megan_summary:
      type: boolean
      description: Specify whether to generate an MEGAN summary file

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - txt:
      type: file
      description: Compressed text file
      pattern: "*.txt.gz"
  - megan_summary:
      type: file
      description: Optionally generated MEGAN summary file
      pattern: "*.megan"

authors:
  - "@jfy133"