application: fuzztran [
  documentation: "Search for patterns in protein sequences (translated)"
  groups: "Nucleic:Motifs, Protein:Motifs"
  gui: "yes"
  batch: "yes"
  cpu: "medium"
]

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

  seqall: sequence [
    parameter: "Y"
    type: "dna"
  ]

  pattern: pattern [
    standard: "Y"
    information: "Search pattern"
    help: "The standard IUPAC one-letter codes for the amino acids are
           used. \
           The symbol 'x' is used for a position where any amino acid is
           accepted. \
           Ambiguities are indicated by listing the acceptable amino acids
           for a given position, between square parentheses '[ ]'. For
           example: [ALT] stands for Ala or Leu or Thr. \
           Ambiguities are also indicated by listing between a pair of curly
           brackets '{ }' the amino acids that are not accepted at a gven
           position. For example: {AM} stands for any amino acid except Ala
           and Met. \
           Each element in a pattern is separated from its neighbor by a '-'.
           (Optional in fuzztran) \
           Repetition of an element of the pattern can be indicated by
           following that element with a numerical value or a numerical range
           between parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4)
           corresponds to x-x or x-x-x or x-x-x-x. \
           When a pattern is restricted to either the N- or C-terminal of a
           sequence, that pattern either starts with a '<' symbol or
           respectively ends with a '>' symbol. \
           A period ends the pattern. (Optional in fuzztran). \
           For example, [DE](2)HS{P}X(2)PX(2,4)C"
    type: "protein"
    pmismatch: "0"
  ]

endsection: input

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

  list: frame [
    additional: "Y"
    default: "1"
    minimum: "1"
    maximum: "1"
    header: "Translation frames"
    values: "1:1, 2:2, 3:3, F:Forward three frames, -1:-1, -2:-2,
             -3:-3, R:Reverse three frames, 6:All six frames"
    delimiter: ","
    codedelimiter: ":"
    information: "Frame(s) to translate"
  ]

  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: "Code to use"
  ]

endsection: additional

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

  report: outfile [
    parameter: "Y"
    taglist: "str:pat=Pattern_name int:mismatch=Mismatch
              int:frame=Frame int:start=PStart int:end=PEnd
              str:translation=Translation"
    rformat: "table"
    precision: "0"
  ]

endsection: output
