I'm not sure I entirely followed what you want. It sounds like you simply want to make the .jar file executable. If that's the case, you can either right click on the file and from the properties menu check the box that says make executable. Or, from the terminal, just navigate to the file's location and run:
Depending on where you downloaded it, you may need root privileges to do this, but I'm guessing that's probably not going to be the case.
chmod +x NW-E00X_MP3_File_Manager-0.17a.jar
Then to run the file, you can (from the terminal), run:
And it should run. I'm not sure how the java script works. Post back any errors you get, or I totally misunderstood what you're after, and we'll sort it out from there.
java -jar /path/to/file/NW-E00X_MP3_File_Manager-0.17a.jar