X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeotuscommand.h;h=6a7cf8a1e55fa1a5fe5915b4cb6da1c3150729ef;hb=8e3e7b1e124f45cb1f2ca9d764ff67fa9b2e532b;hp=ce1646b649e0ed34894b4bce5fd796421ccbc2f3;hpb=794b3f789d6160c99b75edb9cf9af5cf3df4b9da;p=mothur.git

diff --git a/removeotuscommand.h b/removeotuscommand.h
index ce1646b..6a7cf8a 100644
--- a/removeotuscommand.h
+++ b/removeotuscommand.h
@@ -10,8 +10,6 @@
  *
  */
 
-
-
 #include "command.hpp"
 #include "groupmap.h"
 #include "listvector.hpp"
@@ -23,18 +21,21 @@ public:
 	RemoveOtusCommand(string);	
 	RemoveOtusCommand();
 	~RemoveOtusCommand(){}
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();	
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "remove.otus";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Remove.otus"; }
+	string getDescription()		{ return "outputs a new list file containing the otus NOT containing sequences from the groups specified"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	string accnosfile, groupfile, listfile, outputDir, groups, label;
 	bool abort;
 	vector<string> outputNames, Groups;
-	map<string, vector<string> > outputTypes;
 	GroupMap* groupMap;
 	
 	void readAccnos();