application: supermatcher [
  documentation: "Calculate approximate local pair-wise alignments of
                  larger sequences"
  groups: "Alignment:Local"
  gui: "yes"
  batch: "yes"
  cpu: "medium"
]

section: input [
  information: "Input section"
  type: "page"
]

  seqall: asequence [
    parameter: "Y"
    type: "any"
  ]

  seqset: bsequence [
    parameter: "Y"
    type: "@($(acdprotein) ? stopprotein : nucleotide)"
    aligned: "N"
  ]

  matrixf: datafile [
    additional: "Y"
    information: "Matrix file"
    protein: "$(acdprotein)"
    help: "This is the scoring matrix file used when comparing
           sequences. By default it is the file 'EBLOSUM62' (for proteins) or
           the file 'EDNAFULL' (for nucleic sequences). These files are
           found in the 'data' directory of the EMBOSS installation."
  ]

endsection: input

section: required [
  information: "Required section"
  type: "page"
]

  float: gapopen [
    standard: "Y"
    information: "Gap opening penalty"
    minimum: "0.0"
    maximum: "100.0"
    default: "@($(acdprotein)? 10.0 : 10.0)"
    expected: "10.0 for any sequence type"
  ]

  float: gapextend [
    standard: "Y"
    information: "Gap extension penalty"
    minimum: "0.0"
    maximum: "10.0"
    default: "@($(acdprotein)? 0.5 : 0.5)"
    expected: "0.5 for any sequence type"
  ]

endsection: required

section: additional [
  information: "Additional section"
  type: "page"
]

  integer: width [
    additional: "Y"
    default: "16"
    minimum: "1"
    information: "Alignment width"
  ]

  integer: wordlen [
    additional: "Y"
    default: "6"
    minimum: "3"
    information: "Word length for initial matching"
  ]

endsection: additional

section: output [
  information: "Output section"
  type: "page"
]

  align: outfile [
    parameter: "Y"
    aformat: "simple"
    minseqs: "2"
    maxseqs: "2"
  ]

  outfile: errorfile [
    additional: "Y"
    default: "supermatcher.error"
    help: "Error file to be written to"
    knowntype: "supermatcher error"
    information: "Program supermatcher errors output file"
  ]

endsection: output
