How do I make my list filter in Java usable in Automator as a service?
You will need to use the Run Shell Script task within Automator. The tricky bit will be choosing and passing in the various paths.

Here are a few tutorials for creating this kind of Automator Workflow:


Automator Programming Guide: Creating Shell Script Actions
Creating a Shell Script Automator Action
How to build Mac OS X services with Automator and shell scripting