helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000. \n";
helpString += "The mantel command should be in the following format: mantel(phylip1=veg.dist, phylip2=env.dist).\n";
helpString += "The mantel command outputs a .mantel file.\n";
- helpString += "Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\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();
method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "pearson"; }
string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; }
}