X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setdircommand.h;h=837a8b58053cc7b2f5491d8fb59ba00c7c758328;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=0d12e05be43ce8ec055fa5a9bdc39dad62f9bca2;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/setdircommand.h b/setdircommand.h
index 0d12e05..837a8b5 100644
--- a/setdircommand.h
+++ b/setdircommand.h
@@ -25,15 +25,18 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "set.dir";		}
 	string getCommandCategory()		{ return "General";		}
+	string getOutputFileNameTag(string, string) { return ""; }
 	string getHelpString();	
-	
+	string getCitation() { return "http://www.mothur.org/wiki/Set.dir"; }
+	string getDescription()		{ return "set input, output and default directories"; }
+
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	CommandFactory* commandFactory;
 	string output, input, tempdefault;
-	bool abort;
+	bool abort, debugOnly;
 	vector<string> outputNames;