Diff for "Cytoscape_User_Manual/Command_Line_Arguments"

Differences between revisions 11 and 13 (spanning 2 versions)

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 (not
                       implemented in current release).
 -b,--bundle <file>    Load a BUNDLE plugin jar file or URL (not
                       implemented in current release).
 -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).

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.
-T,--table <file>	This option is used to load all types of table files. CSV, XLS, and XLSX files can all be loaded using the -T option. You can specify as many tables as desired on a single command line.
-p,--plugin <file>	This option is not implemented in the current release.
-b,--bundle <file>	This option is not implemented in the current release.
-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 →
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  Editor: ScooterMorris
  Comment:
+  ← Revision 13 as of 2013-06-22 05:16:21 →
  Size: 3565
  Editor: server2
  Comment: Updated to reflect current release.
-Deletions are marked like this.
+Additions are marked like this.
 Line 10:
- -p,--plugin <file>    Load a SIMPLIFIED plugin jar file/URL.

 -b,--bundle <file>    Load a BUNDLE plugin jar file or URL.
+ -p,--plugin <file>    Load a SIMPLIFIED plugin jar file/URL (not

                       implemented in current release).

 -b,--bundle <file>    Load a BUNDLE plugin jar file or URL (not

                       implemented in current release).
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+Line 19:
+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}}}.
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+Line 25:
-||-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"}}}. ||
+||-T,--table <file> ||This option is used to load all types of table files. CSV, XLS, and XLSX files can all be loaded using the -T option. You can specify as many tables as desired on a single command line. ||

||-p,--plugin <file> ||This option is not implemented in the current release. ||

||-b,--bundle <file> ||This option is not implemented in the current release. ||

||-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}}}. ||