appl: oddcomp [
  documentation: "Finds protein sequence regions with a biased composition"
  groups: "Protein:Motifs"
]

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

endsection: input

section: required [ info: "required Section" type: page ]
infile: compdata  [
  parameter: "Y"
  required: "Y"
  information: "'compseq' file to use for expected word frequencies"
  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."
]

integer: window  [
  parameter: "Y"
  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."
]

endsection: required

section: advanced [ info: "advanced Section" type: page ]
bool: 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."
]

endsection: advanced

section: output [ info: "output Section" type: page ]
outfile: outfile  [
  parameter: "Y"
  extension: "oddcomp"
  help: "This is the results file."
]

endsection: output
