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#ifndef METASTATSCOMMAND_H
#define METASTATSCOMMAND_H
/*
* metastatscommand.h
* Mothur
*
* Created by westcott on 9/16/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "inputdata.h"
#include "sharedrabundvectors.hpp"
#include "sharedclrvectors.hpp"
#include "mothurmetastats.h"
#include "designmap.h"
/**************************************************************************************************/
class MetaStatsCommand : public Command {
public:
MetaStatsCommand(string);
~MetaStatsCommand() = default;
vector<string> setParameters();
string getCommandName() { return "metastats"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "White JR, Nagarajan N, Pop M (2009). Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352. \nhttp://www.mothur.org/wiki/Metastats"; }
string getDescription() { return "detects differentially abundant features in clinical metagenomic samples"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, allLines, pickedGroups;
set<string> labels; //holds labels to be used
string groups, label, inputDir, designfile, sets, sharedfile, clrfile, inputfile, format;
vector<string> Groups, outputNames, Sets;
vector< vector<string> > namesOfGroupCombos;
int iters, processors;
float threshold;
int process(SharedRAbundVectors*&, DesignMap*&);
int process(SharedCLRVectors*&, DesignMap*&);
};
/**************************************************************************************************/
#endif
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