application: gcodoncompiler [
  documentation: "Calculates various kinds of amino acid and codon usage data"
  groups: "Nucleic:Codon usage"
  embassy: "gembassy"
  relations: "EDAM_operation:0286 Codon usage analysis"
  relations: "EDAM_topic:0107 Codon usage analysis"
]

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

  seqall: sequence [
    parameter: "Y"
    type: "nucleotide"
    features: "Y"
    relations: "EDAM_data:0849 Sequence record"
  ]

endsection: input

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

  boolean: translate [
    information: "Include to translate using standard codon table"
    default: "N"
  ]

  boolean: startcodon [
    information: "Include to include start codon"
    default: "N"
  ]

  boolean: stopcodon [
    information: "Include to include stop codon"
    default: "N"
  ]

  string: delkey [
    information: "Regular expression to delete key (i.e. amino acids and
                  nucleotides)"
    knowntype: "regular expression"
    default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
  ]

  list: data [
    information: "Kinds of codon usage data. R* hypothesizes amino acids which
                  are not present in the gene"
    values: "A0: Absolute amino acid frequency ('AA');
             A1: Relative amino acid frequency ('RAAU');
             C0: Absolute codon frequency ('AF');
             C1: Relative codon frequency in a complete sequence;
             C2: Relative codon frequency in each amino acid ('RF');
             C3: Relative synonymous codon usage ('RSCU') ;
             C4: Relative adaptiveness; i.e., ratio to maximum of minor codon
                 ('W')
             C5: Maximum (1) or minor (0) codon;
             R0: Absolute codon frequency ('AF');
             R1: Relative codon frequency in a complete sequence;
             R2: Relative codon frequency in each amino acid ('RF');
             R3: Relative synonymous codon usage ('RSCU') ;
             R4: Relative adaptiveness; i.e., ratio to maximum of minor codon
                 ('W')
             R5: Maximum (1) or minor (0) codon"
    default: "R0"
  ]

  boolean: accid [
    information: "Include to use sequence accession ID as query"
    default: "N"
  ]

endsection: advanced

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

  outfile: outfile [
    parameter: "Y"
    information: "Codon usage output file"
    knowntype: "codon usage"
    relations: "EDAM_data:2865 Codon usage bias"
  ]

endsection: output