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"
15 /**************************************************************************************************/
17 class GetOtuLabelsCommand : public Command {
19 GetOtuLabelsCommand(string);
20 GetOtuLabelsCommand();
21 ~GetOtuLabelsCommand(){}
23 vector<string> setParameters();
24 string getCommandName() { return "get.otulabels"; }
25 string getCommandCategory() { return "OTU-Based Approaches"; }
27 string getHelpString();
28 string getOutputPattern(string);
29 string getCitation() { return "http://www.mothur.org/wiki/Get.otulabels"; }
30 string getDescription() { return "Can be used with output from classify.otu, otu.association, or corr.axes to select specific otus."; }
33 void help() { m->mothurOut(getHelpString()); }
37 string outputDir, accnosfile, constaxonomyfile, otucorrfile, corraxesfile;
38 vector<string> outputNames;
41 int readClassifyOtu();
42 int readOtuAssociation();
46 /**************************************************************************************************/