There is a good example of GATE usage from java. Probably it does exactly what you want. BatchProcessApp.java. In particular: loading pipeline is done with lines
// load the saved application
CorpusController application =
(CorpusController)PersistenceManager.loadObjectFromFile(gappFile);
pipeli executed with
// run the application
application.execute();
Code is informative, clear and could be easy changed for your particular needs. The oxygen of open source project :)