X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.h;h=c6d65037516c495f391ceb983273b1b9a20010e1;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=eb0ca8f7832e5f1877a172fa0449a3ae29e5416f;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/readotucommand.h b/readotucommand.h
index eb0ca8f..c6d6503 100644
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -10,27 +10,27 @@
  */
 
 #include "command.hpp"
-#include "readotu.h"
 #include "inputdata.h"
 #include "groupmap.h"
 #include "sharedcommand.h"
 
-class GlobalData;
-
 class ReadOtuCommand : public Command {
 public:
 	ReadOtuCommand(string);
 	ReadOtuCommand();
-	~ReadOtuCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~ReadOtuCommand() {}
+	
+	vector<string> setParameters() {  return outputNames; } //dummy doesn't really do anything
+	string getCommandName()			{ return "read.otu";	}
+	string getCommandCategory()		{ return "Hidden";	}
+	string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like collect.shared."; }	
+	string getCitation() { return "http://www.mothur.org/wiki/Read.otu"; }
+	string getDescription()		{ return "read.otu"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	GlobalData* globaldata;
 	InputData* input;
 	Command* shared;
 	GroupMap* groupMap;