application: wossinput [
  documentation: "Finds programs by EDAM input data"
  groups: "Ontology:EDAM, Documentation"
    relations: "EDAM:0000219 topic Annotation"
    relations: "EDAM:0000088 topic Literature and documentation"
    relations: "EDAM:0000515 operation Data retrieval (tool annotation)"
]

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

  string: identifier [
      default: ""
      parameter: "Y"
      information: "Identifier(s) to search for in ontology"
      knowntype: "keyword"
    relations: "EDAM:0000968 data Keyword"
  ]

endsection: input





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

  boolean: explode [
    additional: "Y"
    default: "N"
    information: "Use the expanded group names"
    help: "The groups that EMBOSS applications belong to have two
           forms, exploded and not exploded. The exploded group names are
           more numerous and often vaguely phrased than the non-exploded
           ones. The exploded names are formed from definitions of the group
           names that start like NAME1:NAME2 and which are then expanded into
           many combinations of the names as: 'NAME1', 'NAME2', 'NAME1
           NAME2', NAME2 NAME1'. The non-expanded names are simply like:
           'NAME1 NAME2'."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: showkeywords [
    additional: "Y"
    default: "N"
    information: "Show keywords with program documentation"
    outputmodifier: "Y"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

endsection: additional





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

  boolean: sensitive [
    default: "N"
    information: "Increase sensitivity of search"
    help: "By default, the query keywords are matched against the EDAM
          term names (and synonyms) only. This option also matches the
	  keywords against the EDAM term definitions and will therefore
	  (typically) report more matches."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: subclasses [
    default: "Y"
    information: "Include subclasses of hits"
    help: "Extend the query matches to include all terms which are
           specialisations (EDAM sub-classes) of the matched type."
    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"
  ]


  boolean: emboss [
    default: "Y"
    information: "Search the EMBOSS programs"
    help: "If you use this option then EMBOSS program documentation
           will be searched. If this option is set to be false, then only the
           EMBASSY programs will be searched (if the -embassy option is
           true). EMBASSY programs are not strictly part of EMBOSS, but use
           the same code libraries and share the same look and feel, but are
           generally developed by people who wish the programs to be outside
           of the GNU Public Licence scheme"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: embassy [
    default: "Y"
    information: "Search the EMBASSY programs"
    help: "If you use this option then EMBASSY program documentation
           will be searched. If this option is set to be false, then only the
           EMBOSS programs will be searched (if the -emboss option is true).
           EMBASSY programs are not strictly part of EMBOSS, but use the
           same code libraries and share the same look and feel, but are
           generally developed by people who wish the programs to be outside
           of the GNU Public Licence scheme"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  string: showembassy [
    default: ""
    information: "Show programs in one EMBASSY package"
    help: "If you use this option then this EMBASSY package program
           documentation will be searched. EMBASSY programs are not strictly
           part of EMBOSS, but use the same code libraries and share the same
           look and feel, but are generally developed by people who wish the
           programs to be outside of the GNU Public Licence scheme"
    knowntype: "embassy package"
    relations: "EDAM:0001195 identifier Tool name (EMBASSY package)"
  ]

  boolean: colon [
    default: "N"
    information: "Put a colon in the group name between two
                  levels"
    help: "The groups that EMBOSS applications belong to up to two
           levels, for example the primary group 'ALIGNMENT' has several
           sub-groups, or second-level groups, e.g.: CONSENSUS, DIFFERENCES,
           DOT PLOTS, GLOBAL, LOCAL, MULTIPLE. To aid programs that parse the
           output of wossname that require the names of these subgroups, a
           colon ':' will be placed between the first and second level of the
           group name if this option is true. Note: This does not apply if
           the group names have been exploded with the 'explode' option."
    outputmodifier: "Y"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: gui [
    default: "N"
    information: "Only report those applications that can run
                  in a GUI"
    help: "This option is intended to help those who are designing
           Graphical User Interfaces to the EMBOSS applications. Some EMBOSS
           programs are inappropriate for running in a GUI, these include
           other menu programs and interactive editors. This option allows
           you to only report those programs that can be run from a GUI"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

endsection: advanced




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

  outfile: outfile [
    additional: "Y"
    default: "stdout"
    knowntype: "tool metadata"
    information: "Tool metadata output file"
    relations: "EDAM:0000958 data Tool metadata"
  ]

  section: htmlsection [
    information: "Html section"
    type: "frame"
  ]

    toggle: html [
      additional: "Y"
      default: "N"
      information: "Format the output for HTML"
      help: "If you are sending the output to a file, this will format
             it for displaying as a table in a WWW document."
      outputmodifier: "Y"
    relations: "EDAM:0002527 data Parameter or primitive"
    ]

  endsection: htmlsection

  boolean: groups [
    additional: "Y"
    default: "N"
    information: "Output only the group names"
    help: "If you use this option, then only the group names will be
           output to the file"
    outputmodifier: "Y"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: alphabetic [
    additional: "Y"
    default: "N"
    information: "Output an alphabetic list of programs"
    help: "If you use this option, then you will get a single list of
           the program names and descriptions instead of the programs being
           listed in their functional groups."
    outputmodifier: "Y"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

endsection: output