X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=systemcommand.h;h=6dc09ef75690b43eb0e5045788308c1a4d26d93b;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=892ac96268baeb2557c51cc67dd0fc571ea4dbfa;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/systemcommand.h b/systemcommand.h
index 892ac96..6dc09ef 100644
--- a/systemcommand.h
+++ b/systemcommand.h
@@ -18,14 +18,17 @@ class SystemCommand : public Command {
 	public:
 	
 		SystemCommand(string);	
-		SystemCommand() { abort = true; calledHelp = true; }
+		SystemCommand() { setParameters(); abort = true; calledHelp = true; }
 		~SystemCommand(){}
 	
-		vector<string> setParameters() { return outputNames; } //dummy does not do anything
+		vector<string> setParameters();
 		string getCommandName()			{ return "system";		}
 		string getCommandCategory()		{ return "General";		}
-		string getHelpString();	
-	
+        string getOutputFileNameTag(string, string) { return ""; }
+        string getHelpString();	
+		string getCitation() { return "http://www.mothur.org/wiki/System"; }
+		string getDescription()		{ return "execute system commands from within mothur"; }
+
 		int execute(); 
 		void help() { m->mothurOut(getHelpString()); }