appl: cpgplot [
  documentation: "Plot CpG rich areas"
  groups: "Nucleic:CpG Islands"
]

section: input [ info: "input Section" type: page ]
seqall: sequence  [
  parameter: "Y"
  type: "DNA"
]

endsection: input

section: required [ info: "required Section" type: page ]
integer: window  [
  required: "Y"
  minimum: "1"
  maximum: "$(sequence.end)"
  default: "100"
  information: "Window size"
  help: "The percentage CG content and the Observed frequency of CG is calculated within a window whose size is set by this parameter. The window is moved down the sequence and these statistics are calculated at each postition that the window is moved to."
]

integer: shift  [
  required: "Y"
  minimum: "1"
  maximum: "$(window)"
  default: "1"
  information: "Window shift increment"
  help: "This determines the number of bases that the window is moved each time after values of the percentage CG content and the Observed frequency of CG are calculated within the window."
]

integer: minlen  [
  required: "Y"
  minimum: "1"
  maximum: "$(sequence.end)"
  default: "200"
  information: "Minimum length of an island"
  help: "This sets the minimum length that a CpG island has to be before it is reported."
]

float: minoe  [
  required: "Y"
  minimum: "0."
  maximum: "10."
  default: "0.6"
  information: "Minimum observed/expected"
  help: "This sets the minimum average observed to expected ratio of C plus G to CpG in a set of 10 windows that are required before a CpG island is reported."
]

float: minpc  [
  required: "Y"
  minimum: "0."
  maximum: "100."
  default: "50."
  information: "Minimum percentage"
  help: "This sets the minimum average percentage of G plus C a set of 10 windows that are required before a CpG island is reported."
]

endsection: required

section: output [ info: "output Section" type: page ]
outfile: outfile  [
  parameter: "Y"
  help: "This sets the name of the file holding the report of the input sequence name, CpG island parameters and the output details of any CpG islands that are found."
]

xygraph: graph  [
  parameter: "Y"
  multiple: "3"
]

bool: obsexp  [
  default: "Y"
  information: "Show observed/expected threshold line"
  help: "If this is set to true then the graph of the observed to expected ratio of C plus G to CpG within a window is displayed."
]

bool: cg  [
  default: "Y"
  information: "Show CpG rich regions"
  help: "If this is set to true then the graph of the regions which have been determined to be CpG islands is displayed."
]

bool: pc  [
  default: "Y"
  information: "Show percentage line"
  help: "If this is set to true then the graph of the percentage C plus G within a window is displayed."
]

featout: featout  [
  parameter: "N"
  information: "feature file for output"
  help: "File for output features"
]

endsection: output

