added ignore option to oligos files for make.contigs, trim.seqs, trim.flows

[mothur.git] / phylotypecommand.h

diff --git a/phylotypecommand.h b/phylotypecommand.h
index 36e679f28aab41ec31848084b117845a9ecab12c..7fe10af58dde8ae842be2496376b3569df49bd29 100644 (file)
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -24,10 +24,14 @@ public:
        ~PhylotypeCommand(){}
        
        vector<string> setParameters();
-       string getCommandName()                 { return "phylotype";                           }
-       string getCommandCategory()             { return "OTU-Based Approaches";        }
-       string getHelpString(); 
+       string getCommandName()                 { return "phylotype";           }
+       string getCommandCategory()             { return "Clustering";          }
        
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
+       string getDescription()         { return "cluster your sequences into OTUs based on their classifications"; }
+
        int execute();
        void help() { m->mothurOut(getHelpString()); }