# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: "famsa_align"
description: Aligns sequences using FAMSA
keywords:
  - alignment
  - MSA
  - genomics
tools:
  - "famsa":
      description: "Algorithm for large-scale multiple sequence alignments"
      homepage: "https://github.com/refresh-bio/FAMSA"
      documentation: "https://github.com/refresh-bio/FAMSA"
      tool_dev_url: "https://github.com/refresh-bio/FAMSA"
      doi: "10.1038/srep33964"
      licence: ["GPL v3"]
      identifier: biotools:famsa
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'test']`
    - fasta:
        type: file
        description: Input sequences in FASTA format
        pattern: "*.{fa,fasta}"
        ontologies:
          - edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
          - edam: http://edamontology.org/format_1929 # FASTA
  - - meta2:
        type: map
        description: |
          Groovy Map containing tree information
          e.g. `[ id:'test_tree']`
    - tree:
        type: file
        description: Input guide tree in Newick format
        pattern: "*.{dnd}"
        ontologies:
          - edam: http://edamontology.org/format_2006 # PHYLOGENETIC TREE
  - compress:
      type: boolean
      description: Flag representing whether the output MSA should be compressed. Set
        to true to enable/false to disable compression. Compression is handled by passing
        '-gz' to FAMSA along with any other options specified in task.ext.args.
output:
  alignment:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'test']`
      - "*.aln{.gz,}":
          type: file
          description: Alignment file, in FASTA format. May be gzipped or uncompressed,
            depending on if compress is set to true or false
          pattern: "*.aln{.gz,}"
          ontologies:
            - edam: http://edamontology.org/format_2554 # ALIGNMENT FORMAT TXT
            - edam: http://edamontology.org/format_1921 # ALIGNMENT FORMAT
            - edam: http://edamontology.org/format_1984 # FASTA-ALN
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@luisas"
  - "@JoseEspinosa"
maintainers:
  - "@luisas"
  - "@JoseEspinosa"
