application: pepwindowall [
  documentation: "Draw Kyte-Doolittle hydropathy plot for a protein alignment"
  groups: "Protein:Properties"
    relations: "EDAM_topic:0137 Protein hydropathy"
    relations: "EDAM_operation:0401 Protein hydropathy calculation
                (from sequence)"
]

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

  seqset: sequences [
    parameter: "Y"
    help: "File containing a sequence alignment"
    type: "gapprotein"
    aligned: "Y"
    relations: "EDAM_data:1384 Sequence alignment (protein)"
  ]

  datafile: datafile [
    additional: "Y"
    information: "AAINDEX entry data file"
    directory: "AAINDEX"
    default: "Enakai.dat"
    knowntype: "aaindex data"
    relations: "EDAM_data:1501 Amino acid index"
  ]

endsection: input

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

  integer: window [
    additional: "Y"
    information: "Window size"
    default: "19"
    minimum: "1"
    maximum: "200"
    relations: "EDAM_data:1251 Window size"
  ]

  boolean: normalize [
    additional: "Y"
    information: "Normalize data values"
    default: "N"
    relations: "EDAM_data:2527 Parameter"
  ]
  

endsection: additional

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

  xygraph: graph [
    parameter: "Y"
    multiple: "$(sequences.count)"
    gxtitle: "Sequence"
    gytitle: "Hydropathy"
    gtitle: "Kyte-Doolittle Plot"
    relations: "EDAM_data:1522 Protein sequence hydropathy plot"
    sequence: "Y"
  ]

endsection: output
