added count file to get.oturep, pre.cluster, screen.seqs, tree.shared. made remove...

[mothur.git] / clearcutcommand.h

diff --git a/clearcutcommand.h b/clearcutcommand.h
index 702fd7e14cb80dc57fd62cb0a738bdf3c6fd2bbd..8f3773eef5cafc5b4a18c56da51df9bdb9606be6 100644 (file)
--- a/clearcutcommand.h
+++ b/clearcutcommand.h
@@ -30,8 +30,10 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "clearcut";                    }
        string getCommandCategory()             { return "Hypothesis Testing";  }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
-       string getCitation() { return "The clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. http://www.mothur.org/wiki/Clearcut"; }
+       string getCitation() { return "Sheneman L, Evans J, Foster JA (2006). Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22: 2823-4. \nhttp://www.mothur.org/wiki/Clearcut"; }
+       string getDescription()         { return "create a tree from a fasta or phylip file"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }