application: epestfind [
  documentation: "Finds PEST motifs as potential proteolytic
                  cleavage sites"
  groups: "Protein:Motifs"
]

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

  sequence: sequence [
    parameter: "Y"
    type: "protein"
    help: "Protein sequence USA to be analysed."
  ]

  datafile: mwdata [
    additional: "Y"
    default: "Emolwt.dat"
    information: "Molecular weights data file"
    knowntype: "molecular weights"
  ]

endsection: input

section: required [
  information: "Required section"
  type: "page"
]

  integer: window [
    standard: "Y"
    default: "10"
    help: "Minimal distance between positively charged amino acids."
    information: "Window length"
    maximum: "$(sequence.length)"
    minimum: "2"
  ]

  selection: order [
    standard: "Y"
    button: "Y"
    casesensitive: "N"
    default: "score"
    delimiter: ","
    header: "Sort order of results"
    help: "Name of the output file which holds the results of the
           analysis. Results may be sorted by length, position and score."
    information: "Sort order of results"
    maximum: "1"
    minimum: "1"
    values: "length, position, score"
  ]

endsection: required

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

  float: threshold [
    additional: "Y"
    default: "+5.0"
    help: "Threshold value to discriminate weak from potential PEST
           motifs. Valid PEST motifs are discriminated into 'poor' and
           'potential' motifs depending on this threshold score. By default,
           the default value is set to +5.0 based on experimental data.
           Alterations are not recommended since significance is a matter of
           biology, not mathematics."
    information: "Threshold score"
    maximum: "+55.0"
    minimum: "-55.0"
    precision: "2"
  ]

endsection: additional

section: advanced [
  information: "Advanced section"
  type: "page"
]

  boolean: mono [
    default: "N"
    information: "Use monoisotopic weights"
  ]

  boolean: potential [
    default: "Y"
    help: "Decide whether potential PEST motifs should be printed."
    information: "Display potential PEST motifs"
  ]

  boolean: poor [
    default: "Y"
    help: "Decide whether poor PEST motifs should be printed."
    information: "Display poor PEST motifs"
  ]

  boolean: invalid [
    default: "N"
    help: "Decide whether invalid PEST motifs should be printed."
    information: "Display invalid PEST motifs"
  ]

  boolean: map [
    default: "Y"
    help: "Decide whether PEST motifs should be mapped to sequence."
    information: "Display PEST motifs map"
  ]

endsection: advanced

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

  outfile: outfile [
    parameter: "Y"
    help: "Name of file to which results will be written."
    knowntype: "epestfind output"
  ]

  xygraph: graph [
    standard: "Y"
    multiple: "1"
  ]

endsection: output
