X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removerarecommand.h;h=2cab7be6fa870d763de76a559b4dfbb72823cfb6;hb=af9291809910b6ddf617490ed5c16254b77b449f;hp=fa22f7a53e6c5149af4c1c1a51504cfb77e9b04e;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/removerarecommand.h b/removerarecommand.h
index fa22f7a..2cab7be 100644
--- a/removerarecommand.h
+++ b/removerarecommand.h
@@ -26,13 +26,18 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "remove.rare";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Remove.rare"; }
+	string getDescription()		{ return "removes rare sequences from a sabund, rabund, shared or list and group file"; }
+
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	string sabundfile, rabundfile, sharedfile, groupfile, listfile, outputDir, groups, label;
+	string sabundfile, rabundfile, sharedfile, groupfile, countfile, listfile, outputDir, groups, label;
 	int nseqs, allLines;
 	bool abort, byGroup;
 	vector<string> outputNames, Groups;