You can use Ant to run a workbench with no interface and run specified Ant scripts.
In the root of the com.ibm.etools.j2ee.ant plugin is a sample batch file called runANT.bat. This .bat file will run a "headless" workbench (no user interface for the development environment) and run a specified ANT script file (example.xml). The ANT script file must be a fully qualified name.