name: last_dotplot
description: Makes a dotplot (Oxford Grid) of pair-wise sequence alignments
keywords:
  - LAST
  - plot
  - pair
  - 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/last-dotplot.rst
      tool_dev_url: https://gitlab.com/mcfrith/last
      doi: ""
      licence: ["GPL-3.0-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, compressed with gzip
      pattern: "*.{maf.gz}"
  - format:
      type: value
      description: Output format (PNG or GIF).

output:
  - png:
      type: file
      description: Pairwise alignment dot plot image, in PNG format.
      pattern: "*.png"
  - gif:
      type: file
      description: Pairwise alignment dot plot image, in GIF format.
      pattern: "*.gif"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@charles-plessy"