application: wordfinder [
  documentation: "Match large sequences against one or more
                  other sequences"
  groups: "Alignment:Local"
  gui: "yes"
  batch: "yes"
  cpu: "medium"
    relations: "EDAM:0000182 topic Sequence alignment"
    relations: "EDAM:0000288 operation Sequence word comparison"
    relations: "EDAM:0000493 operation Pairwise sequence alignment (local)"
]

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

  seqset: asequence [
    parameter: "Y"
    type: "any"
    aligned: "N"
    relations: "EDAM:0000849 data Sequence record"
  ]

  seqall: bsequence [
    parameter: "Y"
    type: "@($(acdprotein) ? stopprotein : nucleotide)"
    relations: "EDAM:0000849 data Sequence record"
  ]

  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."
    relations: "EDAM:0000874 data Comparison matrix"
  ]

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"
    relations: "EDAM:0001397 data Gap opening penalty"
  ]

  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"
    relations: "EDAM:0001398 data Gap extension penalty"
  ]

endsection: required

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

  integer: width [
    additional: "Y"
    default: "16"
    minimum: "1"
    information: "Alignment width"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  integer: wordlen [
    additional: "Y"
    default: "6"
    minimum: "3"
    information: "Word length for initial matching"
    relations: "EDAM:0001250 data Word size"
  ]

  integer: limitmatch [
    additional: "Y"
    default: "0"
    minimum: "0"
    information: "Maximum match score (zero for no limit)"
    relations: "EDAM:0001401 data Match reward score"
  ]

  integer: limitalign [
    additional: "Y"
    default: "0"
    minimum: "0"
    information: "Maximum alignment length (zero for no limit)"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  integer: lowmatch [
    additional: "Y"
    default: "0"
    minimum: "0"
    information: "Minimum match score (zero for no limit)"
    relations: "EDAM:0001401 data Match reward score"
  ]

  integer: lowalign [
    additional: "Y"
    default: "0"
    minimum: "0"
    information: "Minimum alignment length (zero for no limit)"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

endsection: additional

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

  align: outfile [
    parameter: "Y"
    aformat: "simple"
    minseqs: "2"
    maxseqs: "2"
    relations: "EDAM:0001381 data Sequence alignment (pair)"
  ]

  outfile: errorfile [
    additional: "Y"
    default: "wordfinder.error"
    help: "Error file to be written to"
    knowntype: "wordfinder error"
    information: "Program wordfinder errors output file"
    relations: "EDAM:0001678 data Tool log"
  ]

endsection: output