appl: pepwheel [
  documentation: "Shows protein sequences as helices"
  groups: "Display, Protein:2D Structure"
]

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

endsection: input

section: output [ info: "output Section" type: page ]
bool: wheel  [
  default: "Y"
  information: "Plot the wheel"
]

integer: steps  [
  optional: "Y"
  minimum: "2"
  maximum: "100"
  default: "18"
  information: "Number of steps"
  help: "The number of residues plotted per turn is this value divided by the 'turns' value."
]

integer: turns  [
  optional: "Y"
  minimum: "1"
  maximum: "100"
  default: "5"
  information: "Number of turns"
  help: "The number of residues plotted per turn is the 'steps' value divided by this value."
]

section: amphipathicsection [ info: "amphipathic Section" type: frame ]
bool: amphipathic  [
  information: "Prompt for amphipathic residue marking"
  help: "If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified using the qualifiers '-squares', '-diamonds' and '-octags'."
]

string: squares  [
  optional: "@(!$(amphipathic))"
  default: "ILVM"
  information: "Mark as squares"
  help: "By default the aliphatic residues ILVM are marked with squares."
]

string: diamonds  [
  optional: "@(!$(amphipathic))"
  default: "DENQST"
  information: "Mark as diamonds"
  help: "By default the residues DENQST are marked with diamonds."
]

string: octags  [
  optional: "@(!$(amphipathic))"
  default: "HKR"
  information: "Mark as octagons"
  help: "By default the positively charged residues HKR are marked with octagons."
]

endsection: amphipathicsection

section: datasection [ info: "datasection Section" type: frame ]
bool: data  [
  required: "N"
  default: "N"
  information: "Display as data"
  help: "Output the match data to a file instead of plotting it"
]

outfile: outfile  [
  required: "$(data)"
  nullok: "Y"
]

graph: graph  [
  required: "@(!$(data))"
  gxtitle: "$(sequence.name)"
]

endsection: datasection

endsection: output

