application: dotmatcher [
  documentation: "Draw a threshold dotplot of two sequences"
  groups: "Alignment:Dot plots"
    relations: "EDAM:0000159 topic Sequence comparison"
    relations: "EDAM:0000490 operation Dotplot plotting"
]

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

endsection: input

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

  integer: windowsize [
    additional: "Y"
    information: "Window size over which to test threshold"
    default: "10"
    minimum: "3"
    relations: "EDAM:0001251 data Window size"
  ]

  integer: threshold [
    additional: "Y"
    information: "Threshold"
    default: "23"
    minimum: "0"
    relations: "EDAM:0002146 data Threshold"
  ]

endsection: additional

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

  toggle: stretch [
    default: "N"
    information: "Stretch plot"
    help: "Display a non-proportional graph"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  graph: graph [
    standard: "@(!$(stretch))"
    gtitle: "Dotmatcher: $(asequence.usa) vs $(bsequence.usa)"
    gxtitle: "$(asequence.name)"
    gytitle: "$(bsequence.name)"
    relations: "EDAM:0000862 data Dotplot"
  ]

  xygraph: xygraph [
    standard: "$(stretch)"
    gtitle: "Dotmatcher: $(asequence.usa) vs $(bsequence.usa)"
    gxtitle: "$(asequence.name)"
    gytitle: "$(bsequence.name)"
    relations: "EDAM:0000862 data Dotplot"
  ]

endsection: output