application: dotmatcher [
  documentation: "Draw a threshold dotplot of two sequences"
  groups: "Alignment:Dot plots"
]

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

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

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

  matrix: matrixfile [
    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: windowsize [
    additional: "Y"
    information: "Window size over which to test threshhold"
    default: "10"
    minimum: "3"
  ]

  integer: threshold [
    additional: "Y"
    information: "Threshold"
    default: "23"
    minimum: "0"
  ]

endsection: additional

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

  toggle: stretch [
    default: "N"
    information: "Stretch plot"
    help: "Display a non-proportional graph"
  ]

  graph: graph [
    standard: "@(!$(stretch))"
    gtitle: "Dotmatcher: $(asequence.usa) vs $(bsequence.usa)"
    gxtitle: "$(asequence.name)"
    gytitle: "$(bsequence.name)"
  ]

  xygraph: xygraph [
    standard: "$(stretch)"
    gtitle: "Dotmatcher: $(asequence.usa) vs $(bsequence.usa)"
    gxtitle: "$(asequence.name)"
    gytitle: "$(bsequence.name)"
  ]

endsection: output