1 #ifndef READOTUCOMMAND_H
2 #define READOTUCOMMAND_H
7 * Created by Sarah Westcott on 1/20/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 #include "command.hpp"
14 #include "inputdata.h"
16 #include "sharedcommand.h"
20 class ReadOtuCommand : public Command {
22 ReadOtuCommand(string);
25 vector<string> getRequiredParameters();
26 vector<string> getValidParameters();
27 vector<string> getRequiredFiles();
28 map<string, vector<string> > getOutputFiles() { return outputTypes; }
33 GlobalData* globaldata;
37 string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups, outputDir, ordergroupfile, relAbundfile;
38 vector<string> Groups, outputNames;
39 map<string, vector<string> > outputTypes;
42 set<string> labels; //holds labels to be used