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The OBITools3 syntax

Celine Mercier edited this page 2020-07-24 16:23:20 +02:00

• Basic syntax:

    obi command [options] input_URI output_URI
  

• A URI (Uniform Resource Identifier) is a simple way to identify the input and output of a command. For a file, it's simply the path to the file. For a view, it can be the path to the view file in the DMS:

    path_to_my_dms.obidms/VIEWS/my_view.obiview
  

  Or a simplified version:

    path_to_my_dms/my_view
  

  Any hybrid of those 2 works too.

• The - URI can be used to write the result of a command to standard output.

• View names must be unique within a DMS, in other words, views can not be overwritten.

• All tools accept different input and output DMS.

• If the output DMS is not given, the input DMS is used.

• For a taxonomy, both those and their hybrids work:

    path_to_my_dms.obidms/TAXONOMY/my_taxonomy
    path_to_my_dms/taxonomy/my_taxonomy
  

• obi -h gives a list of all the commands.

• obi command -h prints the help of the command.

• obi --version prints the version of the OBITools3 installed.

• Autocompletion of commands and views is available (by pressing tab after 'obi')