The commandTool plugin provides a simple command-line interface to Cytoscape using the CyCommands API. Any plugin that registers commands will be available through commandTool. commandTool provides two main functions: first, it can pop-up a **Command Line Dialog** that allows the user to type commands into Cytoscape and see the results in a "Reply Log". Second, and arguably more useful, it will read script files and execute them. Each line in the script file is a command that is sent to a plugin. Script files may be entered on the Cytoscape command line using the "-S" flag to Cytoscape, or through the "Run script..." menu item under **Plugins→Command Tool**. commandTool uses the CyCommand API to provide help. "help" by itself will list all of the command classes (or namespaces) and "help " followed by a namespace will list all of the commands supported by that namespace. Details of a specific command are available by typing "help " followed by the namespace and command (e.g. "help layout force-directed"). commandTool registers the "commandtool" namespace and supports a single command: run, which takes a file argument. Here is the help for the commandtool run command from commandtool:
**help commandtool run**
commandtool run: Run a command script from a file
Arguments:
[file=value]
