From ee5198c58fed8df58f935235d929069fc619478d Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Fri, 13 Dec 2019 11:31:35 +0100 Subject: [PATCH] mercier created page: The OBITools3 syntax --- The-OBITools3-syntax.md | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 The-OBITools3-syntax.md diff --git a/The-OBITools3-syntax.md b/The-OBITools3-syntax.md new file mode 100644 index 0000000..fafd420 --- /dev/null +++ b/The-OBITools3-syntax.md @@ -0,0 +1,32 @@ +* 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') \ No newline at end of file