added make.lefse command. fixed bug in make.contigs with trimming reverse barcodes...

[mothur.git] / makelefsecommand.h

diff --git a/makelefsecommand.h b/makelefsecommand.h
new file mode 100644 (file)
index 0000000..8270635
--- /dev/null
+++ b/makelefsecommand.h
@@ -0,0 +1,55 @@
+//
+//  makelefse.h
+//  Mothur
+//
+//  Created by SarahsWork on 6/3/13.
+//  Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__makelefse__
+#define __Mothur__makelefse__
+
+#include "mothurout.h"
+#include "command.hpp"
+#include "inputdata.h"
+#include "sharedutilities.h"
+#include "phylosummary.h"
+
+/**************************************************************************************************/
+
+class MakeLefseCommand : public Command {
+public:
+    MakeLefseCommand(string);
+    MakeLefseCommand();
+    ~MakeLefseCommand(){}
+    
+    vector<string> setParameters();
+    string getCommandName()                    { return "make.lefse";                  }
+    string getCommandCategory()                { return "General";             }
+    
+    string getOutputPattern(string);
+       string getHelpString();
+    string getCitation() { return "http://huttenhower.sph.harvard.edu/galaxy/root?tool_id=lefse_upload http://www.mothur.org/wiki/Make.lefse"; }
+    string getDescription()            { return "creates LEfSe input file"; }
+    
+    int execute();
+    void help() { m->mothurOut(getHelpString()); }
+    
+private:
+    bool abort, allLines, otulabel, hasGroupInfo;
+    string outputDir;
+    vector<string> outputNames, Groups;
+    string sharedfile, designfile, constaxonomyfile, relabundfile, scale, label, inputFile;
+    
+    int runRelabund(map<string, consTax2>&, vector<SharedRAbundFloatVector*>&);
+    
+    vector<SharedRAbundFloatVector*> getRelabund();
+    vector<SharedRAbundFloatVector*> getSharedRelabund();
+};
+
+/**************************************************************************************************/
+
+
+
+
+#endif /* defined(__Mothur__makelefse__) */