}
out << "help=" << newHelpString << endl;
+ //remove /n from citation string since gui reads line by line
+ string mycitationString = thisCommand->getCitation();
+ string newCitationString = "";
+ for (int i = 0; i < mycitationString.length(); i++) {
+ if (mycitationString[i] != '\n') { newCitationString += mycitationString[i]; }
+ }
+ out << "citation=" << newCitationString << endl;
+
+ out << "description=" << thisCommand->getDescription() << endl;
+
//outputTypes - makes something like outputTypes=fasta-name-qfile
map<string, vector<string> > thisOutputTypes = thisCommand->getOutputFiles();
map<string, vector<string> >::iterator itTypes;