application: garnier [
  documentation: "Predicts protein secondary structure using GOR method"
  groups: "Protein:2D Structure"
    relations: "EDAM:0000178 topic Protein secondary structure prediction"
    relations: "EDAM:0000267 operation Protein secondary structure prediction"
]

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

  seqall: sequence [
    parameter: "Y"
    type: "PureProtein"
    relations: "EDAM:0002886 data Sequence record (protein)"
  ]

endsection: input

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

  integer: idc [
    default: "0"
    minimum: "0"
    maximum: "6"
    information: "Index decision constants parameter"
    help: "In their paper, GOR mention that if you know something
           about the secondary structure content of the protein you are
           analyzing, you can do better in prediction. 'idc' is an index into
           a set of arrays, dharr[] and dsarr[], which provide 'decision
           constants' (dch, dcs), which are offsets that are applied to the
           weights for the helix and sheet (extend) terms. So, idc=0 says
           don't use the decision constant offsets, and idc=1 to 6 indicates
           that various combinations of dch,dcs offsets should be used."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

endsection: advanced

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

  report: outfile [
    parameter: "Y"
    rformat: "tagseq"
    taglist: "str:garnier"
    relations: "EDAM:0000876 data Protein features (secondary structure)"
  ]

endsection: output