application: cutseq [
  documentation: "Remove a section from a sequence"
  groups: "Edit"
    relations: "EDAM_topic:0091 Data handling"
    relations: "EDAM_operation:0369 Sequence cutting"
]

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

  sequence: sequence [
    parameter: "Y"
    type: "gapany"
    relations: "EDAM_data:0849 Sequence record"
  ]

endsection: input

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

  integer: from [
    standard: "Y"
    default: "$(sequence.begin)"
    minimum: "$(sequence.begin)"
    maximum: "$(sequence.end)"
    failrange: "N"
    trueminimum: "N"
    information: "Start of region to delete"
    help: "This is the start position (inclusive) of the section of
           the sequence that you wish to remove."
    expected: "Start of sequence (0)"
    relations: "EDAM_data:1016 Sequence position"
  ]

  integer: to [
    standard: "Y"
    default: "$(sequence.end)"
    maximum: "$(sequence.end)"
    minimum: "$(from)"
    failrange: "N"
    trueminimum: "N"
    information: "End of region to delete"
    help: "This is the end position (inclusive) of the section of the
           sequence that you wish to remove."
    expected: "End of sequence (0)"
    relations: "EDAM_data:1016 Sequence position"
  ]

endsection: required

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

  seqout: outseq [
    parameter: "Y"
    relations: "EDAM_data:0849 Sequence record"
  ]

endsection: output
