There are some tutorial pages and actual Java code under the org.gstreamer.example source package. You can also check the tutorial page (
https://code.google.com/p/gstreamer-java/wiki/Tutorials) and how to launch gst-launch like pipeline from the command line (
https://code.google.com/p/gstreamer-java/wiki/CommandLine). As to how to describe the pipeline or which elements you should use, there is plenty of documentation for the actual gstreamer implementation - searching the web with the key words 'gstreamer pipeline example matroska' will likely lead to relevant pages with pipeline examples.