X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setcurrentcommand.h;h=effc266fc0dfaccd13d5d1e1fdbe6c348d4428d6;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=5a40e4a20f97377e86d973c2412cc17e12e3fcb0;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/setcurrentcommand.h b/setcurrentcommand.h
index 5a40e4a..effc266 100644
--- a/setcurrentcommand.h
+++ b/setcurrentcommand.h
@@ -23,8 +23,12 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "set.current";	}
 	string getCommandCategory()		{ return "General";		}
-	string getHelpString();	
 	
+	string getHelpString();	
+    string getOutputPattern(string){ return ""; }	
+	string getCitation() { return "http://www.mothur.org/wiki/Set.current"; }
+	string getDescription()		{ return "set current files for mothur"; }
+
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
@@ -36,8 +40,8 @@ private:
 	string clearTypes;
 	vector<string> types;
 	
-	string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
-	string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile;
+	string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile, summaryfile;
+	string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 
 	
 };