application: stretcher [
  documentation: "Needleman-Wunsch rapid global alignment of two sequences"
  groups: "Alignment:Global"
    relations: "EDAM:0000182 topic Sequence alignment"
    relations: "EDAM:0000494 operation Pairwise sequence alignment (global)"
]

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

  sequence: asequence [
    parameter: "Y"
    type: "any"
    relations: "EDAM:0000849 data Sequence record"
  ]

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

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

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

  integer: gapextend [
    additional: "Y"
    information: "Gap length penalty"
    default: "@($(acdprotein)? 2 : 4)"
    minimum: "0"
    valid: "Positive integer"
    expected: "2 for protein, 4 for nucleic"
    relations: "EDAM:0001398 data Gap extension penalty"
  ]

endsection: additional

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

  align: outfile [
    parameter: "Y"
    aformat: "markx0"
    minseqs: "2"
    maxseqs: "2"
    aglobal: "Y"
    relations: "EDAM:0001381 data Sequence alignment (pair)"
  ]

endsection: output