name: "tcoffee_seqreformat"
description: Reformats files with t-coffee
keywords:
  - reformatting
  - alignment
  - genomics
tools:
  - "tcoffee":
      description: "A collection of tools for Computing, Evaluating and Manipulating
        Multiple Alignments of DNA, RNA, Protein Sequences and Structures."
      homepage: "http://www.tcoffee.org/Projects/tcoffee/"
      documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html"
      tool_dev_url: "https://github.com/cbcrg/tcoffee"
      doi: "10.1006/jmbi.2000.4042"
      licence: ["GPL v3"]
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'test' ]`
    - infile:
        type: file
        description: Input file to be reformatted
output:
  - formatted_file:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'test' ]`
      - ${prefix}.txt:
          type: file
          description: Formatted file
          pattern: "*"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@luisas"
  - "@JoseEspinosa"
