1 #ifndef GETOTUSCOMMAND_H
2 #define GETOTUSCOMMAND_H
8 * Created by westcott on 11/10/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
15 #include "command.hpp"
17 #include "listvector.hpp"
19 class GetOtusCommand : public Command {
23 GetOtusCommand(string);
27 vector<string> setParameters();
28 string getCommandName() { return "get.otus"; }
29 string getCommandCategory() { return "OTU-Based Approaches"; }
31 string getHelpString();
32 string getOutputPattern(string);
33 string getCitation() { return "http://www.mothur.org/wiki/Get.otus"; }
34 string getDescription() { return "outputs a new list file containing the otus containing sequences from the groups specified"; }
38 void help() { m->mothurOut(getHelpString()); }
42 string accnosfile, groupfile, listfile, outputDir, groups, label;
44 vector<string> outputNames, Groups;
48 int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);