comparison GEMBASSY-1.0.3/acd/greporiter.acd @ 0:8300eb051bea draft

Initial upload

0:8300eb051bea

application: greporiter [
  documentation: "Gets the positions of replication origin and terminus"
  groups: "Nucleic:Composition"
  embassy: "gembassy"
  relations: "EDAM_topic:3073 Nucleic acid feature detection"
  relations: "EDAM_operation:0415 Nucleic acid feature prediction"
]

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

  seqall: sequence [
    parameter: "Y"
    type: "nucleotide"
    features: "Y"
    relations: "EDAM_data:0849 Sequence record"
  ]

endsection: input

section: advanced [
  information: "Advanced section"
  type: "page"
]

  boolean: oriloc [
    information: "Include Oriloc for prediction"
    default: "N"
  ]

  boolean: gcskew [
    information: "Include to use GC skew shift-point for prediction"
    default: "N"
  ]

  integer: difthreshold [
    information: "Distance between the GC skew shift point and predicted dif
                  site expressed as the precentage of genome size, used as a
                  threshold to retrieve dif sequence from the database"
    default: "0"
  ]

  boolean: dbonly [
    information: "Include to only use values available in databases and to
                  suppress prediction"
    default: "N"
  ]

  boolean: accid [
    information: "Include to use sequence accession ID as query"
    default: "N"
  ]

endsection: advanced

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

  outfile: outfile [
    parameter: "Y"
    relations: "EDAM_data:3127 Nucleic acid features (replication and
                recombination)"
  ]

endsection: output