1 #ifndef GETSABUNDCOMMAND_H
2 #define GETSABUNDCOMMAND_H
8 * Created by Sarah Westcott on 6/2/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
14 #include "command.hpp"
15 #include "inputdata.h"
16 #include "sabundvector.hpp"
18 class GetSAbundCommand : public Command {
20 GetSAbundCommand(string);
22 ~GetSAbundCommand() {}
24 vector<string> setParameters();
25 string getCommandName() { return "get.sabund"; }
26 string getCommandCategory() { return "OTU-Based Approaches"; }
27 string getHelpString();
28 string getCitation() { return "http://www.mothur.org/wiki/Get.sabund"; }
29 string getDescription() { return "creates a sabund file"; }
32 void help() { m->mothurOut(getHelpString()); }
35 string filename, format, inputfile, listfile, rabundfile, outputDir;
39 vector<string> outputNames;
42 set<string> labels; //holds labels to be used