application: infoseq [
  documentation: "Display basic information about sequences"
  groups: "Information"
]

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

  seqall: sequence [
    parameter: "Y"
    type: "gapany"
  ]

endsection: input

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

  boolean: columns [
    default: "Y"
    information: "Print information in neat, aligned columns."
    help: "Set this option on (Y) to print the sequence information
           into neat, aligned columns in the output file. Alternatively,
           leave it unset (N), in which case the information records will be
           delimited by a character, which you may specify by using the
           -delimiter option. In other words, if -columns is set on, the
           -delimiter option is overriden."
  ]

  string: delimiter [
    default: "|"
    information: "Delimiter of records in text output file"
    help: "This string, which is usually a single character only, is
           used to delimit individual records in the text output file. It
           could be a space character, a tab character, a pipe character or
           any other character or string."
    knowntype: "output delimiter"
  ]

endsection: advanced

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

  outfile: outfile [
    additional: "Y"
    default: "stdout"
    knowntype: "infoseq output"
    help: "If you enter the name of a file here then this program will
           write the sequence details into that file."
  ]

  boolean: html [
    additional: "Y"
    default: "N"
    information: "Format output as an HTML table"
    outputmodifier: "Y"
  ]

  boolean: only [
    default: "N"
    information: "Display the specified columns"
    help: "This is a way of shortening the command line if you only
           want a few things to be displayed. Instead of specifying: \
           '-nohead -noname -noacc -notype -nopgc -nodesc' \
           to get only the length output, you can specify \
           '-only -length'"
  ]

  boolean: heading [
    default: "Y"
    information: "Display column headings"
  ]

  boolean: usa [
    default: "@(!$(only))"
    information: "Display the USA of the sequence"
  ]

  boolean: database [
    default: "@(!$(only))"
    information: "Display 'database' column"
  ]

  boolean: name [
    default: "@(!$(only))"
    information: "Display 'name' column"
  ]

  boolean: accession [
    default: "@(!$(only))"
    information: "Display 'accession' column"
  ]

  boolean: gi [
    default: "N"
    information: "Display 'GI' column"
  ]

  boolean: version [
    default: "N"
    information: "Display 'version' column"
  ]

  boolean: type [
    default: "@(!$(only))"
    information: "Display 'type' column"
  ]

  boolean: length [
    default: "@(!$(only))"
    information: "Display 'length' column"
  ]

  boolean: pgc [
    default: "@(!$(only))"
    information: "Display 'percent GC content' column"
  ]

  boolean: description [
    default: "@(!$(only))"
    information: "Display 'description' column"
  ]

endsection: output