tools.yaml

minimap2:
  exec: default
  label: "Minimap2 v2.24"
  command_line: "{exe} -t {threads} {options} -o {out} {target} {query}"
  all_vs_all: "{exe} -t {threads} {options} -o {out} -X {target} {target}"
  max_memory: 40
  threads: 4
  parser: !!null
  split_before: True
  help: "Better for low similar fasta files"
  order: 0
  options:
    -
      group: repeat
      label: Repeatedness
      type: radio
      help: "Trade-off between alignment precision and computation requirements (CPU Time + RAM) by ignoring the top fraction of most frequent minimizers"
      hint: |
        For large genomes keep the "Repeatedness" parameter set to "Many repeats".
        If not your job may be killed because of time limit or memory limit crossing.
      entries:
        -
          key: few
          label: "few repeats"
          value: "-f 0.0002"
          help: "-f 0.0002"
          default: True
        -
          key: some
          label: "some repeats"
          value: "-f 0.002"
          help: "-f 0.002"
        -
          key: many
          label: "many repeats"
          value: "-f 0.02"
          help: "-f 0.02"

mashmap:
  exec: default
  label: "Mashmap v2.0"
  command_line: "{exe} -t {threads} -r {target} -q {query} -o {out}"
  all_vs_all: !!null
  max_memory: 20
  threads: 4
  parser: mashmap2paf
  split_before: False
  help: "Faster for high similar fasta files"
  order: 1
  options: !!null