helpString += "otu.hierarchy(list=yourListFile, label=yourLabels).\n";
helpString += "Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n";
helpString += "The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n";
- helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
return helpString;
}
catch(exception& e) {
//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();
abort = true;
}
}else if (listFile == "not open") { abort = true; }
+ else { m->setListFile(listFile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
//go through each bin in "big" otu and output the bins in "little" otu which created it
for (int i = 0; i < lists[1].getNumBins(); i++) {
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
string names = lists[1].get(i);
out.close();
- if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();