//loop through each command outputting info
for (it = commands.begin(); it != commands.end(); it++) {
- if (m->control_pressed) { m->mothurOut("[ERROR]: did not complete making the file."); m->mothurOutEndLine(); out.close(); remove((output+".temp").c_str()); }
+ if (m->control_pressed) { m->mothurOut("[ERROR]: did not complete making the file."); m->mothurOutEndLine(); out.close(); m->mothurRemove((output+".temp")); }
Command* thisCommand = commandFactory->getCommand(it->first);
}
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;
out2.close();
m->appendFiles(output+".temp", output);
- remove((output+".temp").c_str());
+ m->mothurRemove((output+".temp"));
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();