- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+
+ vector<string> setParameters();
+ string getCommandName() { return "cluster"; }
+ string getCommandCategory() { return "Clustering"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nSchloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6.\nhttp://www.mothur.org/wiki/Cluster"; }
+ string getDescription() { return "cluster your sequences into OTUs using a distance matrix"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }