Yes, sure!
You can pass the ROM filename as the main argument to the emulator.
But remember, Javatari can load ROMs from anywhere including the web, so the format for the ROM filenames must always be a valid URL. In the case of a local file, you must include the protocol "file:/" in the filename.
For example, to run the latest version executable JAR and start a ROM in Windows:
> javaw -jar javatari40.jar file:/c:/roms/enduro.bin
or simply:
> start javatari40.jar file:/c:/roms/enduro.bin
It also supports drag and drop of files and URLs, even inside the browser when deployed as an Applet.
See this website for example, you can simply drag the game images on the right into the emulator screen:
How are you planning to offer/integrate Javatari in your project?
Regards,
Paulo