application: stretcher [
  documentation: "Needleman-Wunsch rapid global alignment of two sequences"
  groups: "Alignment:Global"
]

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

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

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

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

  integer: gapopen [
    additional: "Y"
    information: "Gap penalty"
    default: "@($(acdprotein)? 12 : 16)"
    minimum: "0"
    valid: "Positive integer"
    expected: "12 for protein, 16 for nucleic"
  ]

  integer: gapextend [
    additional: "Y"
    information: "Gap length penalty"
    default: "@($(acdprotein)? 2 : 4)"
    minimum: "0"
    valid: "Positive integer"
    expected: "2 for protein, 4 for nucleic"
  ]

endsection: additional

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

  align: outfile [
    parameter: "Y"
    aformat: "markx0"
    minseqs: "2"
    maxseqs: "2"
    aglobal: "Y"
  ]

endsection: output
