application: density [
  documentation: "Draw a nucleic acid density plot"
  groups: "Nucleic:Composition"
]

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

  seqall: seqall [
    parameter: "Y"
    type: "dna"
  ]

endsection: input

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

  integer: window [
    additional: "Y"
    minimum: "1"
    default: "100"
    information: "Window length"
  ]

endsection: additional

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

  toggle: quad [
    default: "N"
    information: "Produce graphic showing individual bases"
  ]

  toggle: dual [
    default: "N"
    information: "Produce AT vs GC graphic"
  ]

  xygraph: qgraph [
    standard: "$(quad)"
    multiple: "4"
    information: "Quad (A+C+G+T) graph"
  ]

  xygraph: dgraph [
    standard: "$(dual)"
    multiple: "2"
    information: "Dual (AT+GC) graph"
  ]

  report: outfile [
    standard: "@(@(!$(quad)) & @(!$(dual)))"
    taglist: "float:a float:c float:g float:t float:at float:gc"
    rformat: "table"
    knowntype: "density output"
    nullok: "Y"
    nulldefault: "@($(quad) | $(dual))"
  ]

endsection: output
