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//
// 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 "phylosummary.h"
/**************************************************************************************************/
class MakeLefseCommand : public Command {
public:
MakeLefseCommand(string);
~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;
vector<string> outputNames, Groups;
string sharedfile, designfile, constaxonomyfile, relabundfile, scale, label, inputFile;
int runRelabund(map<int, consTax2>&, SharedRAbundFloatVectors*&);
SharedRAbundFloatVectors* getRelabund();
SharedRAbundFloatVectors* getSharedRelabund();
};
/**************************************************************************************************/
#endif /* defined(__Mothur__makelefse__) */
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