application: extractseq [
  documentation: "Extract regions from a sequence"
  groups: "Edit"
    relations: "EDAM:0000091 topic Data handling"
    relations: "EDAM:0000369 operation Sequence cutting"
]

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

  sequence: sequence [
    parameter: "Y"
    type: "any"
    relations: "EDAM:0000849 data Sequence record"
  ]

endsection: input

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

  range: regions [
    standard: "Y"
    default: "$(sequence.begin)-$(sequence.end)"
    information: "Regions to extract (eg: 4-57,78-94)"
    help: "Regions to extract. \
           A set of regions is specified by a set of pairs of positions. \
           The positions are integers. \
           They are separated by any non-digit, non-alpha character. \
           Examples of region specifications are: \
           24-45, 56-78 \
           1:45, 67=99;765..888 \
           1,5,8,10,23,45,57,99"
    expected: "Whole sequence"
    relations: "EDAM:0001017 data Sequence range"
  ]

endsection: required

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

  boolean: separate [
    additional: "Y"
    default: "N"
    information: "Write regions to separate sequences"
    help: "If this is set true then each specified region is written
           out as a separate sequence. The name of the sequence is created
           from the name of the original sequence with the start and end
           positions of the range appended with underscore characters between
           them, eg: XYZ region 2 to 34 is written as: XYZ_2_34"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

endsection: additional

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

  seqoutall: outseq [
    parameter: "Y"
    relations: "EDAM:0000849 data Sequence record"
  ]

endsection: output