name: last_mafconvert
description: Converts MAF alignments in another format.
keywords:
  - LAST
  - convert
  - alignment
  - MAF
tools:
  - last:
      description: LAST finds & aligns related regions of sequences.
      homepage: https://gitlab.com/mcfrith/last
      documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/
      tool_dev_url: https://gitlab.com/mcfrith/last
      doi: ""
      licence: ['GPL v3-or-later']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - maf:
      type: file
      description: Multiple Aligment Format (MAF) file, optionally compressed with gzip
      pattern: "*.{maf.gz,maf}"
  - format:
      type: value
      description: Output format (one of axt, blast, blasttab, chain, gff, html, psl, sam, or tab)

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
  - axt_gz:
      type: file
      description: Gzipped pairwise alignment in Axt (Blastz) format (optional)
      pattern: "*.axt.gz"
  - blast_gz:
      type: file
      description: Gzipped pairwise alignment in blast format (optional)
      pattern: "*.blast.gz"
  - blasttab_gz:
      type: file
      description: Gzipped pairwise alignment in blasttab format (optional)
      pattern: "*.blasttab.gz"
  - chain_gz:
      type: file
      description: Gzipped pairwise alignment in UCSC chain format (optional)
      pattern: "*.chain.gz"
  - gff_gz:
      type: file
      description: Gzipped pairwise alignment in GFF format (optional)
      pattern: "*.gff.gz"
  - html_gz:
      type: file
      description: Gzipped pairwise alignment in HTML format (optional)
      pattern: "*.html.gz"
  - psl_gz:
      type: file
      description: Gzipped pairwise alignment in PSL (BLAT) format (optional)
      pattern: "*.psl.gz"
  - SAM:
      type: file
      description: Gzipped pairwise alignment in SAM format (optional)
      pattern: "*.sam.gz"
  - tab:
      type: file
      description: Gzipped pairwise alignment in TAB format (optional)
      pattern: "*.tab.gz"

authors:
  - "@aleksandrabliznina"