You cannot 'call' a jar file in FitNesse. You can add the Java classes contained in the jars to the classes available to FitNesse (its class path) and then call the Java classes contained in them from the wiki.
To add the jars to the classpath you can use !path
, e.g. !path /myETLjars/*.jar
To call the classes inside them can be a bit more complex, depending on how they work (the Java methods that need to be called to perform the extraction and compare). Maybe you can use a Slim script table?
Or you could, of course, use a FitNesse fixture that allows you to execute command line tools from FitNesse and just execute the two jars you mention and show their output in a wiki table. This is not how I would expect a test to be setup in FitNesse, but certainly possible. My FitNesse fixtures/baseline project does contain a Slim fixture that would allow you to execute a command line tool: execute program test, or you could easily write your own, and I believe similar functionality is also available in Fit fixtures.