A few things:
1. What you're planning to do is contrary to the goal of automated testing because you are requiring user intervention via a GUI - now your tests cannot be run unattended.
2. Reading from an XML file makes your test run slower -- this is not going to be a very good unit test since it crosses a system boundary by accessing the file system. It's fine for a test to read from the file system but then it should be run with the set of integration tests, not as a unit test.
3. If you really need to allow the user to do something before you run the tests, then create a separate program that presents the GUI and reads the XML file. Once the user makes his/her selection, then you can programmatically run JUnit, specifying the user-selected parameters as if they were command line parameters. That way you can have your GUI and still write the test per normal JUnit test conventions. I still think there's something fundamentally wrong with your approach if you need to have a user intervene.
And welcome to the Ranch!