X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clearcutcommand.h;h=817c4a3290804405bd47582d9b3ec5349c182b43;hp=af456566b241a5592b710c01d7d0486090c80705;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/clearcutcommand.h b/clearcutcommand.h
index af45656..817c4a3 100644
--- a/clearcutcommand.h
+++ b/clearcutcommand.h
@@ -11,7 +11,6 @@
  */
 
 #include "command.hpp"
-#include "globaldata.hpp"
 
 /* 
   Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining: 
@@ -31,7 +30,11 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "clearcut";			}
 	string getCommandCategory()		{ return "Hypothesis Testing";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
+	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()); }