The-OBITools3-syntax.md

+* 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.
+
+* 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')
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