application: dbxedam [
  documentation: "Index the EDAM ontology 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"
    default: "edam"
    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: standardname [
    parameter: "Y"
    maxlength: "19"
    minlength: "2"
    default: "$(dbname)"
    information: "Standard database name"
    knowntype: "emboss database name"
    pattern: "[A-z][A-z0-9_]+"
    relations:  "EDAM_identifier:1056 Database name"                          
  ]

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

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

  string: filenames [
    standard: "Y"
    default: "EDAM*.obo"
    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:Synonym;nam:Name;isa:Parent;
             des:Description;ns:Namespace;
             hasin:has_input;hasout:has_output;
             isid:is_identifier_of;isfmt:is_format_of"
    minimum: "1"
    maximum: "10"
    default: "*"
    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"
  ]

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