application: oddcomp [
  documentation: "Identify proteins with specified sequence word composition"
  groups: "Protein:Composition"
    relations: "EDAM_topic:0157 Sequence composition analysis"
    relations: "EDAM_operation:0378 Sequence composition calculation
                (protein)"
]

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

  seqall: sequence [
    parameter: "Y"
    type: "Protein"
    relations: "EDAM_data:2886 Sequence record (protein)"
  ]

  infile: infile [
    parameter: "Y"
    information: "Program compseq output file"
    help: "This is a file in the format of the output produced by
           'compseq' that is used to set the minimum frequencies of words in
           this analysis."
    knowntype: "compseq output"
    relations: "EDAM_data:1261 Sequence composition"
  ]

endsection: input

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

  toggle: fullwindow [
    default: "N"
    information: "Set window size to length of current protein"
    help: "Set this option on (Y) if you want the window size to be
           set to the length of the current protein. Otherwise, leave this
           option unset, in which case you'll be prompted for a window size
           to use."
    relations: "EDAM_data:2527 Parameter"
  ]

  integer: window [
    standard: "@(!$(fullwindow))"
    minimum: "10"
    default: "30"
    information: "Window size to consider (e.g. 30 aa)"
    help: "This is the size of window in which to count. \
           Thus if you want to count frequencies in a 40 aa stretch you
           should enter 40 here."
    relations: "EDAM_data:1251 Window size"
  ]

endsection: required

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

  boolean: ignorebz [
    default: "Y"
    information: "Ignore the amino acids B and Z and just count
                  them as 'Other'"
    help: "The amino acid code B represents Asparagine or Aspartic
           acid and the code Z represents Glutamine or Glutamic acid. \
           These are not commonly used codes and you may wish not to count
           words containing them, just noting them in the count of 'Other'
           words."
    relations: "EDAM_data:2527 Parameter"
  ]

endsection: advanced

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

  outfile: outfile [
    parameter: "Y"
    extension: "oddcomp"
    help: "This is the results file."
    knowntype: "oddcomp output"
    relations: "EDAM_data:1111 EMBOSS listfile"
  ]

endsection: output