//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ command += " > ./commandScreen.output 2>&1";
system(command.c_str());
+ ifstream in;
+ string filename = "./commandScreen.output";
+ m->openInputFile(filename, in, "no error");
+
+ string output = "";
+ while(char c = in.get()){
+ if(in.eof()) { break; }
+ else { output += c; }
+ }
+ in.close();
+
+ m->mothurOut(output); m->mothurOutEndLine();
+ remove(filename.c_str());
+
return 0;
}