Diff for "Cytoscape_User_Manual/Command_Line_Arguments"

Differences between revisions 11 and 12

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: java -Xmx512M -jar cytoscape.jar [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).
 -e,--edge-attrs <file>    Load an edge attributes file (edge attribute format).
 -n,--node-attrs <file>   Load a node attributes file (node attribute format).
 -m,--matrix <file>        Load a node attribute matrix file (table).
 -p,--plugin <file>         Load a plugin jar file, directory of jar files,
                                     plugin class name, or plugin jar URL.
 -P,--props <file>         Load cytoscape properties file (Java properties
                                    format) or individual property: -P name=value.
 -V,--vizmap <file>      Load vizmap properties file (Java properties format).

Any file specified for an option may be specified as either a path or as a URL. For example you can specify a network as a file (assuming that myNet.sif exists in the current working directory): cytoscape.sh -N myNet.sif. Or you can specify a network as a URL: cytoscape.sh -N http://example.com/myNet.sif.

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.
-e,--edge-attrs <file>	This option specifies an edge attributes file. You may specify as many edge attribute files as desired on a single command line.
-n,--node-attrs <file>	This option specifies a node attributes file. You may specify as many node attribute files as desired on a single command line.
-m,--matrix <file>	This option specifies a data matrix file. In a biological context, the data matrix consists of expression data. All data matrix files are read into node attributes. You may specify as many data matrix files as desired on a single command line.
-p,--plugin <file>	This option specifies a cytoscape plugin (.jar) file to be loaded by Cytoscape. This option also subsumes the previous "resource plugin option". You may specify a class name that identifies your plugin and the plugin will be loaded if the plugin is in Cytoscape's CLASSPATH. For example, assuming that the class MyPlugin can be found in the CLASSPATH, you could specify the plugin like this: `cytoscape.sh -p MyPlugin.class`. A final means of specifying plugins is to specify a file name whose contents contain a list of plugin jar files.
-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"`. The property option subsumes previous options -noCanonicalization, -species, and -bioDataServer. Now it would look like: `cytoscape.sh -P defaultSpeciesName=Human -P noCanonicalization=true -P bioDataServer=myServer`.
-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.

Cytoscape_User_Manual/Command_Line_Arguments (last edited 2013-06-25 23:21:52 by server2)

-  ← Revision 11 as of 2012-12-19 00:32:34 →
  Size: 3221
  Editor: ScooterMorris
  Comment:
+  ← Revision 12 as of 2012-12-20 00:26:07 →
  Size: 4460
  Editor: ScooterMorris
  Comment: Meant to edit Cytoscape 3 manual...
-Deletions are marked like this.
+Additions are marked like this.
 Line 4:
-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).
+usage: java -Xmx512M -jar cytoscape.jar [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).

 -e,--edge-attrs <file>    Load an edge attributes file (edge attribute format).

 -n,--node-attrs <file>   Load a node attributes file (node attribute format).

 -m,--matrix <file>        Load a node attribute matrix file (table).

 -p,--plugin <file>         Load a plugin jar file, directory of jar files,

                                     plugin class name, or plugin jar URL.

 -P,--props <file>         Load cytoscape properties file (Java properties

                                    format) or individual property: -P name=value.

 -V,--vizmap <file>      Load vizmap properties file (Java properties format).
-Line 17:
+Line 18:
+Any file specified for an option may be specified as either a path or as a URL.  For example you can specify a network as a file (assuming that myNet.sif exists in the current working directory): {{{cytoscape.sh -N myNet.sif}}}. Or you can specify a network as a URL: {{{cytoscape.sh -N http://example.com/myNet.sif}}}.
-Line 22:
+Line 24:
-||-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"}}}. ||
+||-e,--edge-attrs <file> ||This option specifies an edge attributes file.  You may specify as many edge attribute files as desired on a single command line. ||

||-n,--node-attrs <file> ||This option specifies a node attributes file.  You may specify as many node attribute files as desired on a single command line. ||

||-m,--matrix <file> ||This option specifies a data matrix file.  In a biological context, the data matrix consists of expression data. All data matrix files are read into node attributes. You may specify as many data matrix files as desired on a single command line. ||

||-p,--plugin <file> ||This option specifies a cytoscape plugin (.jar) file to be loaded by Cytoscape. This option also subsumes the previous "resource plugin option".   You may specify a class name that identifies your plugin and the plugin will be loaded if the plugin is in Cytoscape's CLASSPATH.  For example, assuming that the class !MyPlugin can be found in the CLASSPATH, you could specify the plugin like this: {{{cytoscape.sh -p MyPlugin.class}}}.  A final means of specifying plugins is to specify a file name whose contents contain a list of plugin jar files. ||

||-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"}}}.  The property option subsumes previous options -noCanonicalization, -species, and -bioDataServer.  Now it would look like: {{{cytoscape.sh -P defaultSpeciesName=Human -P noCanonicalization=true -P bioDataServer=myServer}}}. ||