# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "clipkit"
description: ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically
  informative sites and removes those that display characteristics poor phylogenetic
  signal.
keywords:
  - alignment
  - trimming
  - phylogeny
tools:
  - "clipkit":
      description: "Alignment trimming software for phylogenetics."
      homepage: "https://jlsteenwyk.com/ClipKIT/"
      documentation: "https://jlsteenwyk.com/ClipKIT/"
      tool_dev_url: "https://github.com/JLSteenwyk/ClipKIT"
      doi: "10.1371/journal.pbio.3001007"
      licence: ["MIT"]
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - aln:
        type: file
        description: Multiple sequence alignment file in various supported formats.
        pattern: "*.{fa,fasta,fa,fna,faa,alnfaa,aln,sto,stk,mauve,alignment,clustal}"
        ontologies: []
  - out_format:
      type: string
      description: Output format (aln,msa,fas,etc.), default is clipkit.
      pattern: "*"
output:
  clipkit:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - ${prefix}.${out_extension}:
          type: file
          description: Trimmed multiple sequence alignment file
          pattern: "*.*"
          ontologies: []
  log:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - ${prefix}.log:
          type: file
          description: Log file with statistics from the tool's execution
          pattern: "*.log"
          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"
