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#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 "inputdata.h"
#include "picrust.hpp"
#include "biomsimple.hpp"
#include "biomhdf5.hpp"
class MakeBiomCommand : public Command {
public:
MakeBiomCommand(string);
~MakeBiomCommand(){}
vector<string> setParameters();
string getCommandName() { return "make.biom"; }
string getCommandCategory() { return "General"; }
string getHelpString();
string getOutputPattern(string);
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, relabundfile, contaxonomyfile, metadatafile, groups, format, label, referenceTax, picrustOtuFile, inputFileName, fileFormat, output;
vector<string> outputNames, Groups;
set<string> labels;
bool abort, allLines, picrust;
void getBiom(SharedRAbundVectors*&, Picrust*, vector<Taxonomy>, vector<string>);
void getBiom(SharedRAbundFloatVectors*&, Picrust*, vector<Taxonomy>, vector<string>);
vector<string> getSampleMetaData(SharedRAbundVectors*&);
vector<string> getSampleMetaData(SharedRAbundFloatVectors*&);
};
#endif
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