2 // filtersharedcommand.h
5 // Created by Sarah Westcott on 1/4/13.
6 // Copyright (c) 2013 Schloss Lab. All rights reserved.
9 #ifndef Mothur_filtersharedcommand_h
10 #define Mothur_filtersharedcommand_h
12 #include "command.hpp"
13 #include "sharedrabundvector.h"
14 #include "inputdata.h"
17 class FilterSharedCommand : public Command {
20 FilterSharedCommand(string);
21 FilterSharedCommand();
22 ~FilterSharedCommand() {}
24 vector<string> setParameters();
25 string getCommandName() { return "filter.shared"; }
26 string getCommandCategory() { return "OTU-Based Approaches"; }
28 string getHelpString();
29 string getOutputPattern(string);
30 string getCitation() { return "http://www.mothur.org/wiki/Filter.shared"; }
31 string getDescription() { return "remove OTUs based on various criteria"; }
34 void help() { m->mothurOut(getHelpString()); }
37 bool abort, pickedGroups, allLines, makeRare;
38 set<string> labels; //holds labels to be used
39 string groups, label, outputDir, sharedfile;
40 vector<string> Groups, outputNames;
41 int minAbund, minTotal, minSamples;
42 float minPercent, minPercentSamples;
44 int processShared(vector<SharedRAbundVector*>&);