1 #ifndef Mothur_getotulabelscommand_h
2 #define Mothur_getotulabelscommand_h
5 // getotulabelscommand.h
8 // Created by Sarah Westcott on 5/21/12.
9 // Copyright (c) 2012 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "inputdata.h"
15 #include "listvector.hpp"
16 #include "sharedrabundvector.h"
18 /**************************************************************************************************/
20 class GetOtuLabelsCommand : public Command {
22 GetOtuLabelsCommand(string);
23 GetOtuLabelsCommand();
24 ~GetOtuLabelsCommand(){}
26 vector<string> setParameters();
27 string getCommandName() { return "get.otulabels"; }
28 string getCommandCategory() { return "OTU-Based Approaches"; }
30 string getHelpString();
31 string getOutputPattern(string);
32 string getCitation() { return "http://www.mothur.org/wiki/Get.otulabels"; }
33 string getDescription() { return "Can be used with output from classify.otu, otu.association, or corr.axes to select specific otus."; }
36 void help() { m->mothurOut(getHelpString()); }
40 string outputDir, accnosfile, constaxonomyfile, otucorrfile, corraxesfile, listfile, sharedfile, label;
41 vector<string> outputNames;
44 vector<SharedRAbundVector*> lookup;
46 int readClassifyOtu();
47 int readOtuAssociation();
55 /**************************************************************************************************/