Put your command and parameters in an array:
String[] command = {
"/Users/brianallison/Documents/Java/RELAP5 GUI/issrs/relap5.x",
"-i", "Choose your input file",
"-r", "",
"-o", ""
};
Then execute using Runtime#exec(String[] cmdarray):
Runtime.getRuntime().exec(command);
This answer has been put together after reading your other two questions from today, herehere and herehere.