application: wordfinder [
  documentation: "Match large sequences against one or more
                  other sequences"
  groups: "Alignment:Local"
  gui: "yes"
  batch: "yes"
  cpu: "medium"
]

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

  seqset: asequence [
    parameter: "Y"
    type: "any"
    aligned: "N"
  ]

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

  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: "1000.0"
    default: "@($(acdprotein)? 30.0 : 30.0)"
    expected: "10.0 for any sequence type"
  ]

  float: gapextend [
    standard: "Y"
    information: "Gap extension penalty"
    minimum: "0.0"
    maximum: "10.0"
    default: "@($(acdprotein)? 1.5 : 1.5)"
    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"
  ]

  integer: limitmatch [
    additional: "Y"
    default: "0"
    minimum: "0"
    information: "Maximum match score (zero for no limit)"
  ]

  integer: limitalign [
    additional: "Y"
    default: "0"
    minimum: "0"
    information: "Maximum alignment length (zero for no limit)"
  ]

  integer: lowmatch [
    additional: "Y"
    default: "0"
    minimum: "0"
    information: "Minimum match score (zero for no limit)"
  ]

  integer: lowalign [
    additional: "Y"
    default: "0"
    minimum: "0"
    information: "Minimum alignment length (zero for no limit)"
  ]

endsection: additional

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

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

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

endsection: output
