1 #ifndef Mothur_getcoremicrobiomcommand_h
2 #define Mothur_getcoremicrobiomcommand_h
6 // GetCoreMicroBiomeCommand.h
9 // Created by John Westcott on 5/8/12.
10 // Copyright (c) 2012 Schloss Lab. All rights reserved.
14 #include "command.hpp"
15 #include "inputdata.h"
17 /**************************************************************************************************/
19 class GetCoreMicroBiomeCommand : public Command {
21 GetCoreMicroBiomeCommand(string);
22 GetCoreMicroBiomeCommand();
23 ~GetCoreMicroBiomeCommand(){}
25 vector<string> setParameters();
26 string getCommandName() { return "get.coremicrobiome"; }
27 string getCommandCategory() { return "OTU-Based Approaches"; }
28 //commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
30 string getHelpString();
31 string getOutputPattern(string);
32 string getCitation() { return "http://www.mothur.org/wiki/Get.coremicrobiome"; }
33 string getDescription() { return "determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances"; }
36 void help() { m->mothurOut(getHelpString()); }
39 string relabundfile, sharedfile, inputFileName, format, output;
41 vector<string> Groups;
45 vector<string> outputNames;
48 int createTable(vector<SharedRAbundFloatVector*>&);
52 /**************************************************************************************************/