application: eyinoyang [
  documentation: "Reports O-(beta)-GlcNAc attachment sites"
  groups: "Protein:Motifs"
  embassy: "cbstools"
]

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

  seqset: sequence [
    parameter: "Y"
    type: "any"
    aligned: "Y"
    relations: "EDAM: Sequence alignment data"                             
  ]

endsection: input

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

endsection: required

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

  boolean: plot [
    default: "N"
    information: "Produce graphics"
    relations: "EDAM: Generic boolean"                                     
  ]

  list: format [
    header:   "Output format"
    default: "short"
    minimum: "1"
    maximum: "1"
    values: "short:short, long:long"
    delimiter: ","
    codedelimiter: ":"
    information: "Format"
    relations: "EDAM: Generic string array"                                
  ]

  boolean: netphos [
    default: "N"
    information: "Run netphos and predict Yin-Yang sites"
    relations: "EDAM: Generic boolean"                                     
  ]

  float: threshold [
    default: "0.5"
    minimum: "0.0"
    maximum: "1.0"
    information: "Report netphos only scores above this value"
    relations: "EDAM: Generic float"                                       
  ]

endsection: advanced

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

  outfile: outfile [
    parameter: "Y"
    knowntype: "eyinoyang output"
    relations:  "EDAM:Protein post-translation modification site report"   
  ]

endsection: output
