+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+ map<string, string>::iterator it;
+
+ ValidParameters validParameter;
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ string commandOption = validParameter.validFile(parameters, "command", false);
+ if (commandOption == "not found") { commandOption = ""; }
+ else { command = commandOption; }
+
+ if ((option == "") && (commandOption == "")) { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
+ else if (commandOption == "") {