X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeotuscommand.h;h=3a52a39f120a0d2af788478df3a590c64a7f9306;hb=ce8794490ab1d83adcdb2b92e0302a1e43e17adf;hp=872b2c8caf1e7b082a040b2da15960f39dcb27e0;hpb=259b6adf51ef0639cafd88cf862e4ffd5e0c7576;p=mothur.git

diff --git a/removeotuscommand.h b/removeotuscommand.h
index 872b2c8..3a52a39 100644
--- a/removeotuscommand.h
+++ b/removeotuscommand.h
@@ -21,21 +21,24 @@ 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 getOutputFileNameTag(string, string);
+	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();
 	int readListGroup();
 	int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);