helpString += "The iters parameter allows you to select the number of random configuration to try. Default=10\n";
helpString += "The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12.\n";
helpString += "Example nmds(phylip=yourDistanceFile).\n";
- helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\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();
phylipfile = m->getPhylipFile();
if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setPhylipFile(phylipfile); }
axesfile = validParameter.validFile(parameters, "axes", true);
if (axesfile == "not open") { axesfile = ""; abort = true; }