+
+#include "command.hpp"
+#include "inputdata.h"
+#include "designmap.h"
+
+/**************************************************************************************************/
+
+class LefseCommand : public Command {
+public:
+ LefseCommand(string);
+ LefseCommand();
+ ~LefseCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "lefse"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+
+ string getOutputPattern(string);
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Lefse"; }
+ string getDescription() { return "brief description"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+private:
+ bool abort, allLines;
+ string outputDir, sharedfile, designfile, mclass, subclass, classes;
+ vector<string> outputNames;
+ set<string> labels;
+ float anovaAlpha, wilcoxonAlpha;
+
+ int process(vector<SharedRAbundVector*>&, DesignMap&);
+ vector<int> runKruskalWallis(vector<SharedRAbundVector*>&, DesignMap&);
+ vector<int> runWilcoxon(vector<SharedRAbundVector*>&, DesignMap&, vector<int>);
+
+};
+
+/**************************************************************************************************/
+
+
+
+