//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();
sharedfile = m->getSharedFile();
if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setSharedFile(sharedfile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
in >> inputData;
}
- if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); remove(outputFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); m->mothurRemove(outputFile); return 0; }
if (in.eof() != true) { in >> nextLabel; }
//read the rest of the groups info in
while ((nextLabel == holdLabel) && (in.eof() != true)) {
- if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); remove(outputFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); m->mothurRemove(outputFile); return 0; }
in >> groupN >> num;
count++;
in.close();
out.close();
- if (m->control_pressed) { remove(outputFile.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(outputFile); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();