EDIT: It seems I misunderstood the question. I usually use the term "command line input" to refer to command line arguments given to the process to start with, rather than interactive console input. However...
Handing your real code either a different InputStream or possibly even a Reader or Scanner would indeed help - anything to separate the "getting input" part from the console. You can then fake the input all in one go pretty easily, using a String as input in your test code, and then either converting it to bytes and wrapping those bytes in a ByteArrayInputStream or wrapping the string directly in StringReader.
The downside of this is that there's no easy way of making this "pause" after one command in order to check the results.
You may want to alter the design somewhat so that the part which reads the input is separated from the part which handles the input. The reading part could be a very simple loop, on the order of:
String line;
while ((line = reader.readLine()) != null) {
handleInput(line);
}
You could then potentially leave that part untested by unit tests, or write some relatively primitive tests - but you can then test handleInput extensively, as it's now separated from the input source.
Original answer
If you've extracted the parsing code from the code which really starts the application, it's easy: run that code, and check the results. This will be easiest if you have some sort of class encapsulating the options, of course. For example, your main method might look like this:
public static void main(String[] args) {
Options options = Options.parse(args);
// Use options here
}
Then you can just test Options.parse very easily.
