X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parselistscommand.h;h=84abc85d46e0bc3fddd916a0095c4b45aa44dbd1;hp=065c499ade25c46fb18ef3746fc5c08687c232d6;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/parselistscommand.h b/parselistscommand.h
index 065c499..84abc85 100644
--- a/parselistscommand.h
+++ b/parselistscommand.h
@@ -26,7 +26,11 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "parse.list";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Parse.list"; }
+	string getDescription()		{ return "parses a list file by group"; }
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
@@ -36,10 +40,10 @@ private:
 		
 	ListVector* list;
 	GroupMap* groupMap;
-	InputData* input;
+    CountTable ct;
 	
 	ofstream out;
-	string outputDir, listfile, groupfile, label;
+	string outputDir, listfile, groupfile, label, countfile;
 	set<string> labels;
 	bool abort, allLines;
 	vector<string> outputNames;