--- /dev/null
+#ifndef Mothur_makebiomcommand_h
+#define Mothur_makebiomcommand_h
+
+//
+// makebiomcommand.h
+// Mothur
+//
+// Created by Sarah Westcott on 4/16/12.
+// Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+
+#include "command.hpp"
+#include "sharedrabundvector.h"
+#include "inputdata.h"
+
+
+class MakeBiomCommand : public Command {
+
+public:
+ MakeBiomCommand(string);
+ MakeBiomCommand();
+ ~MakeBiomCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "make.biom"; }
+ string getCommandCategory() { return "General"; }
+ string getHelpString();
+ string getCitation() { return "http://biom-format.org/documentation/biom_format.html, http://www.mothur.org/wiki/Make.biom"; }
+ string getDescription() { return "creates a biom file"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+private:
+
+ string sharedfile, contaxonomyfile, groups, outputDir, format, label;
+ vector<string> outputNames, Groups;
+ set<string> labels;
+
+ bool abort, allLines;
+
+ int getBiom(vector<SharedRAbundVector*>&);
+ vector<string> getMetaData(vector<SharedRAbundVector*>&);
+};
+
+
+#endif