application: epestfind [
  documentation: "Find PEST motifs as potential proteolytic
                  cleavage sites"
  groups: "Protein:Motifs"
  relations: "EDAM_topic:0158 Sequence motifs"
  relations: "EDAM_topic:0767 Protein and peptide identification"
  relations: "EDAM_operation:0422 Protein cleavage site prediction"
]

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

  sequence: sequence [
    parameter: "Y"
    type: "protein"
    help: "Protein sequence USA to be analysed."
    relations: "EDAM_data:2886 Sequence record (protein)"
  ]

  datafile: mwdata [
    additional: "Y"
    default: "Emolwt.dat"
    information: "Molecular weights data file"
    knowntype: "molecular weights"
    relations: "EDAM_data:1505 Amino acid index (molecular weight)"
  ]

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"
    failrange: "N"
    trueminimum: "Y"
    relations: "EDAM_data:1251 Window size"
  ]

  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"
    relations: "EDAM_data:2134 Results sort order"
  ]

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"
    relations: "EDAM_data:2146 Threshold"
  ]

endsection: additional

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

  boolean: mono [
    default: "N"
    information: "Use monoisotopic weights"
    relations: "EDAM_data:2527 Parameter"
  ]

  boolean: potential [
    default: "Y"
    help: "Decide whether potential PEST motifs should be printed."
    information: "Display potential PEST motifs"
    relations: "EDAM_data:2527 Parameter"
  ]

  boolean: poor [
    default: "Y"
    help: "Decide whether poor PEST motifs should be printed."
    information: "Display poor PEST motifs"
    relations: "EDAM_data:2527 Parameter"
  ]

  boolean: invalid [
    default: "N"
    help: "Decide whether invalid PEST motifs should be printed."
    information: "Display invalid PEST motifs"
    relations: "EDAM_data:2527 Parameter"
  ]

  boolean: map [
    default: "Y"
    help: "Decide whether PEST motifs should be mapped to sequence."
    information: "Display PEST motifs map"
    relations: "EDAM_data:2527 Parameter"
  ]

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"
    relations: "EDAM_data:1323 Protein features (cleavage sites)"
  ]

  xygraph: graph [
    standard: "Y"
    multiple: "1"
    relations: "EDAM_data:1323 Protein features (cleavage sites)"
    sequence: "Y"
  ]

endsection: output
