//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
string temp;
else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (listFile == "not open") { abort = true; }
+ else { m->setListFile(listFile); }
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not found") { phylipfile = ""; }
else if (phylipfile == "not open") { abort = true; }
- else { distFile = phylipfile; format = "phylip"; }
+ else { distFile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile); }
columnfile = validParameter.validFile(parameters, "column", true);
if (columnfile == "not found") { columnfile = ""; }
else if (columnfile == "not open") { abort = true; }
- else { distFile = columnfile; format = "column"; }
+ else { distFile = columnfile; format = "column"; m->setColumnFile(columnfile); }
if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these?
//give priority to column, then phylip
lineLabel = validParameter.validFile(parameters, "label", false); if (lineLabel == "not found") { lineLabel = ""; }
- sensSpecFileName = listFile.substr(0,listFile.find_last_of('.')) + ".sensspec";
+ sensSpecFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + ".sensspec";
}
}
catch(exception& e) {
if(format == "phylip") { processPhylip(); }
else if(format == "column") { processColumn(); }
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(sensSpecFileName); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
return 0;
}