Cytoscape_User_Manual/Command_Line_Arguments

Cytoscape recognizes a number of optional command line arguments, including run-time specification of network files, attribute files, and session files. This is the output generated when the cytoscape is executed with the "-h" or "--help" flag:

usage: cytoscape.{sh|bat} [OPTIONS]
 -h,--help             Print this message.
 -v,--version          Print the version number.
 -s,--session <file>   Load a cytoscape session (.cys) file.
 -N,--network <file>   Load a network file (any format).
 -T,--table <file>     Load a data table file (any table format).
 -p,--plugin <file>    Load a SIMPLIFIED plugin jar file/URL.
 -b,--bundle <file>    Load a BUNDLE plugin jar file or URL.
 -P,--props <file>     Load cytoscape properties file (Java properties
                       format) or individual property: -P name=value.
 -V,--vizmap <file>    Load vizmap properties file (Cytoscape VizMap
                       format).

Argument	Description
-h,--help	This flag generates the help output you see above and exits.
-v,--version	This flag prints the version number of Cytoscape and exits.
-s,--session <file>	This option specifies a session file to be loaded. Since only one session file can be loaded at a given time, this option may only specified once on a given command line. The option expects a `.cys` Cytoscape session file. It is customary, although not necessary, for session file names to contain the .cys extension.
-N,--network <file>	This option is used to load all types of network files. SIF, GML, and XGMML files can all be loaded using the -N option. You can specify as many networks as desired on a single command line.
-T,--table <file>	This option specifies a table file to be loaded.
-p,--plugin <file>	This option specifies a SIMPLIFIED plugin (.jar) file to be loaded by Cytoscape. Simplified plugins are plugins that do not implement CyActivator directly, but inherit from one of the CyAppAdapters. These plugins are all loaded using the same class loader.
-b,--bundle <file>	This option specifies a BUNDLE plugin (.jar) file to be loaded by Cytoscape. Bundle plugins are plugins that implement CyActivator directly and utilize the OSGi framework to access the Cytoscape API. Each bundle plugin is loaded using it's own class loader, allowing increased isolation from library collision.
-P,--props <file>	This option specifies Cytoscape properties. Properties can be specified either as a properties file (in Java's standard properties format), or as individual properties. To specify individual properties, you must specify the property name followed by the property value where the name and value are separated by the '=' sign. For example to specify the defaultSpeciesName: `cytoscape.sh -P defaultSpeciesName=Human`. If you would like to include spaces in your property, simply enclose the name and value in quotation marks: `cytoscape.sh -P "defaultSpeciesName=Homo Sapiens"`.
-V,--vizmap <file>	This option specifies a visual properties file.

All options described above (including plugins) can be loaded from the GUI once Cytoscape is running.