X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getotuscommand.h;h=c71ab062b431c9ca7945c8e0b8679980058939c8;hp=ec69acb4c0381c6b2b5190abf1a88ae214751647;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=794b3f789d6160c99b75edb9cf9af5cf3df4b9da

diff --git a/getotuscommand.h b/getotuscommand.h
index ec69acb..c71ab06 100644
--- a/getotuscommand.h
+++ b/getotuscommand.h
@@ -23,21 +23,27 @@ public:
 	GetOtusCommand(string);	
 	GetOtusCommand();
 	~GetOtusCommand(){}
-	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 "get.otus";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Get.otus"; }
+	string getDescription()		{ return "outputs a new list file containing the otus 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&);