appl: primers [
  documentation: "Simple version of primer3 to pick PCR primers"
  groups: "Nucleic:Primers"
]

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

seqall: sequence  [
  parameter: "Y"
  type: "dna"
  help: "The sequence from which to choose primers. The sequence must be presented 5' -> 3'"
]

endsection:  input

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

range: target  [
  optional: "Y"
  default: ""
  information: "Target region(s)"
  help: "If one or more Targets is specified then a legal primer pair must flank at least one of them. A Target might be a simple sequence repeat site (for example a CA repeat) or a single-base-pair polymorphism. The value should be a space-separated list of \ <start>,<end> \ pairs where <start> is the index of the first base of a Target, and <end> is the last \ E.g. 50,51 requires primers to surround the 2 bases at positions 50 and 51."
]

endsection:  required

section: advanced  [ info: "advanced section"  type: page ]

integer: minsize  [
  optional: "Y"
  default: "18"
  minimum: "1"
  information: "Primer minimum size"
  help: "Minimum acceptable length of a primer. Must be greater than 0 and less than or equal to MAX-SIZE."
]

integer: maxsize  [
  optional: "Y"
  default: "27"
  minimum: "$(MinSize)"
  maximum: "35"
  information: "Primer maximum size"
  help: "Maximum acceptable length (in bases) of a primer. Currently this parameter cannot be larger than 35. This limit is governed by the maximum oligo size for which Primer3's melting-temperature is valid."
]

float: maxdifftm  [
  optional: "Y"
  default: "100.0"
  information: "Maximum difference in Tm of primers"
  help: "Maximum acceptable (unsigned) difference between the melting temperatures of the forward and reverse primers."
]

endsection:  advanced

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

bool: explainflag  [
  optional: "Y"
  default: "N"
  information: "Explain flag"
  help: "If this flag is non-0, produce LEFT-EXPLAIN and RIGHT-EXPLAIN, output, which are intended to provide information on the number of primer pairs that Primer3 examined, and statistics on the number discarded for various reasons."
]

integer: numreturn  [
  optional: "Y"
  default: "5"
  minimum: "0"
  information: "Number of results to return"
  help: "The maximum number of primer pairs to return. Primer pairs returned are sorted by their 'quality', in other words by the value of the objective function (where a lower number indicates a better primer pair). Caution: setting this parameter to a large value will increase running time."
]

outfile: outfile  [
  parameter: "Y"
]

endsection:  output
