parameters["group"] = "group";
parameters["order"] = "order";
parameters["fasta"] = "fasta";
- parameters["treefile"] = "treefile";
+ parameters["tree"] = "tree";
parameters["fileroot"] = "fileroot";
parameters["cutoff"] = "cutoff";
parameters["method"] = "method";
parameters["format"] = "format";
parameters["precision"] = "precision";
parameters["label"] = "label";
- parameters["line"] = "line";
+ parameters["line"] = "line";
parameters["iters"] = "iters";
parameters["jumble"] = "jumble";
parameters["freq"] = "freq";
- parameters["single"] = "single";
- parameters["rarefaction"] = "rarefaction";
- parameters["sharedrarefaction"] = "sharedrarefaction";
- parameters["shared"] = "shared";
- parameters["summary"] = "summary";
- parameters["sharedsummary"] = "sharedsummary";
+ parameters["abund"] = "abund";
+ parameters["random"] = "random";
+ parameters["groups"] = "groups";
+ parameters["calc"] = "calc";
}
catch(exception& e) {
if ((parameters.find(parameter)) != (parameters.end())) {
return true;
}else{
- cout << parameter << " is not a valid parameter in Mothur." << endl;
+ cout << parameter << " is not a valid parameter in Mothur. Valid parameters are " << endl;
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+
return false;
}