name: "hmmer_eslalimask"
description: Mask multiple sequence alignments
keywords:
  - hmmer
  - alignment
  - mask
tools:
  - "hmmer":
      description: "Biosequence analysis using profile hidden Markov models"
      homepage: http://hmmer.org/
      documentation: http://hmmer.org/documentation.html

      doi: "10.1371/journal.pcbi.1002195"
      licence: ["BSD-3-Clause"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]

  - unmaskedaln:
      type: file
      description: multiple sequence alignment, Stockholm or other formats
      pattern: "*"

  - fmask_rf:
      type: val
      description: Flag to output optional file with final mask of non-gap RF len

  - fmask_all:
      type: val
      description: Flag to output optional file with final mask of full aln len

  - gmask_rf:
      type: val
      description: Flag to output optional file gap-based 0/1 mask of non-gap RF len

  - gmask_all:
      type: val
      description: Flag to output optional file gap-based 0/1 mask of full aln len

  - pmask_rf:
      type: val
      description: Flag to output optional file with PP-based 0/1 mask of non-gap RF len

  - pmask_all:
      type: val
      description: Flag to output optional file with PP-based 0/1 mask of full aln len

  - maskfile:
      type: file
      description: mask file, see program documentation
      pattern: "*"

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"

  - maskedaln:
      type: file
      description: Masked alignment in gzipped Stockholm format
      pattern: "*.sthlm.gz"

  - fmask_rf:
      type: file
      description: File with final mask of non-gap RF len
      pattern: "*.fmask-rf.gz"

  - fmask_all:
      type: file
      description: File with final mask of full aln len
      pattern: "*.fmask-all.gz"

  - gmask_rf:
      type: file
      description: File with gap-based 0/1 mask of non-gap RF len
      pattern: "*.gmask-rf.gz"

  - gmask_all:
      type: file
      description: File with gap-based 0/1 mask of full aln len
      pattern: "*.gmask-all.gz"

  - pmask_rf:
      type: file
      description: File with PP-based 0/1 mask of non-gap RF len
      pattern: "*.pmask-rf.gz"

  - pmask_all:
      type: file
      description: File with PP-based 0/1 mask of full aln len
      pattern: "*.pmask-all.gz"

authors:
  - "@erikrikarddaniel"
