# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "hhsuite_reformat"
description: Reformat a Multiple Sequence Alignment (MSA) file
keywords:
  - reformat
  - MSA
  - hhsuite
  - alignment
tools:
  - "hhsuite":
      description: "HH-suite3 for fast remote homology detection and deep protein annotation"
      homepage: "https://github.com/soedinglab/hh-suite"
      documentation: "https://github.com/soedinglab/hh-suite/wiki"
      tool_dev_url: "https://github.com/soedinglab/hh-suite"
      doi: "10.1371/journal.pone.0082138"
      licence: ["GPL v3"]
      identifier: biotools:hh-suite
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1' ]`
    - aln:
        type: file
        description: Input MSA file
        pattern: "*.{fa,fasta,fas,a2m,a3m,sto,psi,clu,fa.gz,fasta.gz,fas.gz,a2m.gz,a3m.gz,sto.gz,psi.gz,clu.gz}"
        ontologies: []
  - informat:
      type: string
      description: Format of the input MSA file
      enum: ["fas", "a2m", "a3m", "sto", "psi", "clu"]
  - outformat:
      type: string
      description: Format of the output MSA file
      enum: ["fas", "a2m", "a3m", "sto", "psi", "clu"]
output:
  msa:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1' ]`
      - ${prefix}.${outformat}.gz:
          type: file
          description: Gzipped reformatted output MSA file
          pattern: "*.{fas.gz,a2m.gz,a3m.gz,sto.gz,psi.gz,clu.gz}"
          ontologies: []
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@vagkaratzas"
maintainers:
  - "@vagkaratzas"
