Well, personally I'd never use FileWriter as it uses the system default encoding, which is a nasty thing to do most of the time. I prefer FileOutputStream + OutputStreamWriter. However, having said that...
What do you want to pass as the command line argument? The file name? That's easy:
public static void main(String[] args)
{
// Insert error checking here (e.g. args.length == 0)
String note = args[0]; // For the first argument
// Rest of code here
}
If that's not what you mean, please edit your question to clarify it.
Judging by the title, you may be wanting to load from a file instead of from System.in. In that case, you just need to pass in a File object, or an InputStream (such as FileInputStream) or indeed a Readable (such as InputStreamReader). If you're going to pass in a File or InputStream, I'd strongly recommend that you pass in the character encoding name as well. (Quite why it takes it as a string instead of a Charset is beyond me, but the Java API is basically pretty bad when it comes to encodings.)