application: dbxgcg [
  documentation: "Index a GCG formatted database using b+tree indices"
  groups: "Utils:Database indexing"
  gui: "no"
  batch: "yes"
  cpu: "medium"
    relations: "EDAM_topic:0091 Data handling"
    relations: "EDAM_operation:0227 Data indexing"
]

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

  string: dbname [
    parameter: "Y"
    maxlength: "19"
    minlength: "2"
    information: "Basename for index files"
    knowntype: "emboss database name"
    pattern: "[A-z][A-z0-9_]+"
    relations: "EDAM_identifier:1056 Database name"
  ]

  string: dbresource [
    parameter: "Y"
    maxlength: "19"
    minlength: "2"
    information: "Resource name"
    knowntype: "emboss resource name"
    pattern: "[A-z][A-z0-9_]+"
    relations: "EDAM_data:2527 Parameter"
  ]

  list: idformat [
    standard: "y"
    information: "Entry format"
    values: "EMBL:EMBL; SWISS:Swiss-Prot, SpTrEMBL, TrEMBLnew;
             GENBANK:Genbank, DDBJ; PIR:NBRF"
    maximum: "1"
    minimum: "1"
    default: "SWISS"
    relations: "EDAM_identifier:2129 File format name"
  ]

  directory: directory [
    standard: "Y"
    default: "."
    information: "Database directory"
    knowntype: "emboss database directory"
    relations: "EDAM_identifier:1049 Directory name"
  ]

  string: filenames [
    standard: "Y"
    default: "*.seq"
    information: "Wildcard database filename"
    knowntype: "emboss database wildcard filename"
    relations: "EDAM_identifier:1050 File name"
  ]

endsection: input

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

  list: fields [
    standard: "Y"
    information: "Index fields"
    values: "id:ID;acc:Accession number;sv:Sequence Version and
             GI;des:Description;key:Keywords;org:Taxonomy"
    minimum: "1"
    maximum: "6"
    default: "id,acc"
    relations: "EDAM_data:2527 Parameter"
  ]

  boolean: compressed [
    standard: "Y"
    default: "Y"
    information: "Compressed index files"
    relations: "EDAM_data:2527 Parameter"
  ]

endsection: required

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

  string: release [
    default: "0.0"
    maxlength: "9"
    information: "Release number"
    knowntype: "emboss database release"
    relations: "EDAM_data:1670 Database version information"
  ]

  string: date [
    default: "00/00/00"
    valid: "Date string dd/mm/yy"
    information: "Index date"
    pattern: "^([0-9]+.[0-9]+.[0-9]+)?$"
    knowntype: "date"
    relations: "EDAM_data:2156 Date"
  ]

  string: exclude [
    information: "Wildcard filename(s) to exclude"
    knowntype: "filename wildcard"
    relations: "EDAM_identifier:1050 File name"
  ]

  boolean: statistics [
    default: "N"
    information: "Report I/O statistics for each input file"
    relations: "EDAM_data:2527 Parameter"
  ]

endsection: advanced

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

  outdir: indexoutdir [
    default: "."
    information: "Index file output directory"
    knowntype: "emboss database index"
    relations: "EDAM_identifier:1049 Directory name"
  ]

  outfile: outfile [
    standard: "Y"
    knowntype: "log"
    information: "General log output file"
    relations: "EDAM_data:1678 Tool log"
  ]

endsection: output
