application: ontocount [
  documentation: "Count ontology term(s)"
  groups: "Ontology"
    relations: "EDAM:0000089 topic Ontologies"
    relations: "EDAM:0002224 operation Data retrieval (ontology concept)"
]

section: input [
  information: "Input section"
  type: "page"
]
  obo: oboterms [
     default: ""
     parameter: "Y"
     relations: "EDAM:0001087 identifier Ontology term ID"
  ]


endsection: input





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

endsection: additional





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

  boolean: subclasses [
    default: "N"
    information: "Include subclasses of hits"
    help: "Extend the query matches to include all terms which are
           specialisations (sub-classes) of the matched terms."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]


  boolean: obsolete [
    default: "N"
    information: "Include obsolete terms"
    help: "The default behaviour is to not use or return obsolete terms.
           This option if set will include all terms."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]


endsection: advanced





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

  outfile: outfile [
    parameter: "Y"
    default: "stdout"
    knowntype: "ontocount output"
    relations: "EDAM:0002223 data Ontology metadata"
  ]

endsection: output