application: prettyseq [
  documentation: "Write a nucleotide sequence and its translation to file"
  groups: "Nucleic:Translation, Display"
    relations: "EDAM_topic:0108 Translation"
    relations: "EDAM_topic:0092 Data visualisation"
    relations: "EDAM_operation:0371 DNA translation"
    relations: "EDAM_operation:0564 Sequence rendering"
]

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

  sequence: sequence [
    parameter: "Y"
    type: "DNA"
    relations: "EDAM_data:0849 Sequence record"
  ]

endsection: input

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

  range: range [
    standard: "Y"
    information: "Range(s) to translate"
    default: "$(sequence.begin)-$(sequence.end)"
    expected: "Whole sequence"
    relations: "EDAM_data:1017 Sequence range"
  ]

endsection: required

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

  list: table [
    additional: "Y"
    default: "0"
    minimum: "1"
    maximum: "1"
    header: "Genetic codes"
    values: "0:Standard; 1:Standard (with alternative initiation
             codons); 2:Vertebrate Mitochondrial; 3:Yeast Mitochondrial;
             4:Mold, Protozoan, Coelenterate Mitochondrial and
             Mycoplasma/Spiroplasma; 5:Invertebrate Mitochondrial; 6:Ciliate
             Macronuclear and Dasycladacean; 9:Echinoderm Mitochondrial;
             10:Euplotid Nuclear; 11:Bacterial; 12:Alternative Yeast Nuclear;
             13:Ascidian Mitochondrial; 14:Flatworm Mitochondrial;
             15:Blepharisma Macronuclear; 16:Chlorophycean Mitochondrial;
             21:Trematode Mitochondrial; 22:Scenedesmus obliquus;
             23:Thraustochytrium Mitochondrial"
    delimiter: ";"
    codedelimiter: ":"
    information: "Genetic code to use"
    relations: "EDAM_identifier:2128 Genetic code name"
  ]

  boolean: ruler [
    additional: "Y"
    default: "Y"
    information: "Add a ruler"
    relations: "EDAM_data:2527 Parameter"
  ]

  boolean: plabel [
    additional: "Y"
    default: "Y"
    information: "Number translations"
    relations: "EDAM_data:2527 Parameter"
  ]

  boolean: nlabel [
    additional: "Y"
    default: "Y"
    information: "Number DNA sequence"
    relations: "EDAM_data:2527 Parameter"
  ]

endsection: additional

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

  integer: width [
    minimum: "10"
    default: "60"
    information: "Width of screen"
    relations: "EDAM_data:1249 Sequence length"
  ]

endsection: advanced

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

  outfile: outfile [
    parameter: "Y"
    knowntype: "prettyseq output"
    relations: "EDAM_data:1313 Nucleic acid features (coding sequence)"
  ]

endsection: output
