appl: fuzznuc [
  documentation: "Nucleic acid pattern search"
  groups: "Nucleic:Motifs"
]

section: input [ info: "input Section" type: page ]
seqall: sequence  [
  parameter: "Y"
  type: "dna"
]

endsection: input

section: required [ info: "required Section" type: page ]
string: pattern  [
  required: "Y"
  prompt: "Search pattern"
  help: "The standard IUPAC one-letter codes for the nucleotides are used. \ 
The symbol `n' is used for a position where any nucleotide is accepted. \ 
Ambiguities are indicated by listing the acceptable nucleotides for a
given position, between square parentheses `[ ]'.  For example: [ACG]
stands for A or C or G. \ 
Ambiguities are also indicated by listing between a pair of curly
brackets `{ }' the nucleotides that are not accepted at a given
position.  For example: {AG} stands for any nucleotides except A and G. \ 
Each element in a pattern is separated from its neighbor by a `-'.
(Optional in fuzznuc). \ 
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: N(3) corresponds to N-N-N, N(2,4) corresponds to
N-N or N-N-N or N-N-N-N. \ 
When a pattern is restricted to either the 5' or 3' end of a
sequence, that pattern either starts with a `<' symbol or respectively
ends with a `>' symbol. \ 
A period ends the pattern.  (Optional in fuzznuc). \ 
For example, [CG](5)TG{A}N(1,5)C"
]

integer: mismatch  [
  required: "Y"
  default: "0"
  minimum: "0"
  prompt: "Number of mismatches"
]

endsection: required

section: advanced [ info: "advanced Section" type: page ]
bool: complement  [
  optional: "N"
  default: "0"
  prompt: "Search complementary strand"
]

endsection: advanced

section: output [ info: "output Section" type: page ]

report: outfile  [
  parameter: "Y"
  taglist: "int:mismatch=Mismatch"
  rformat: "seqtable"
  precision: 0
]

endsection: output
