There are a growing number of tools based on java packages - perhaps the example in tools/sr_mapping/srma_wrapper.xml could be a useful 'simple' starting point? For more complex scenarios, there are a number of new Picard based java tools (only exposed on test at present) in the galaxy-central source tree under tools/picard that do even more complex integration of multiple outputs into html output files. The relevant jars are all placed in tool-data/shared/jars and that path is passed in the xml command template as something like: --jar="${GALAXY_DATA_INDEX_DIR}/shared/jars/foo.jar" Of course YMMV depending on your specific needs but this approach certainly can be made to work for java packages like Picard and FastQC.