5 // Created by SarahsWork on 6/3/13.
6 // Copyright (c) 2013 Schloss Lab. All rights reserved.
9 #ifndef __Mothur__makelefse__
10 #define __Mothur__makelefse__
12 #include "mothurout.h"
13 #include "command.hpp"
14 #include "inputdata.h"
15 #include "sharedutilities.h"
16 #include "phylosummary.h"
18 /**************************************************************************************************/
20 class MakeLefseCommand : public Command {
22 MakeLefseCommand(string);
26 vector<string> setParameters();
27 string getCommandName() { return "make.lefse"; }
28 string getCommandCategory() { return "General"; }
30 string getOutputPattern(string);
31 string getHelpString();
32 string getCitation() { return "http://huttenhower.sph.harvard.edu/galaxy/root?tool_id=lefse_upload http://www.mothur.org/wiki/Make.lefse"; }
33 string getDescription() { return "creates LEfSe input file"; }
36 void help() { m->mothurOut(getHelpString()); }
39 bool abort, allLines, otulabel, hasGroupInfo;
41 vector<string> outputNames, Groups;
42 string sharedfile, designfile, constaxonomyfile, relabundfile, scale, label, inputFile;
44 int runRelabund(map<string, consTax2>&, vector<SharedRAbundFloatVector*>&);
46 vector<SharedRAbundFloatVector*> getRelabund();
47 vector<SharedRAbundFloatVector*> getSharedRelabund();
50 /**************************************************************************************************/
55 #endif /* defined(__Mothur__makelefse__) */