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"
13 #include "inputdata.h"
15 #include "sharedcommand.h"
17 class ReadOtuCommand : public Command {
19 ReadOtuCommand(string);
23 vector<string> setParameters() { return outputNames; } //dummy doesn't really do anything
24 string getCommandName() { return "read.otu"; }
25 string getCommandCategory() { return "Hidden"; }
26 string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like collect.shared."; }
27 string getCitation() { return "http://www.mothur.org/wiki/Read.otu"; }
28 string getDescription() { return "read.otu"; }
31 void help() { m->mothurOut(getHelpString()); }
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