1 #ifndef REMOVEOTUSCOMMAND_H
2 #define REMOVEOTUSCOMMAND_H
8 * Created by westcott on 11/12/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
15 #include "listvector.hpp"
17 class RemoveOtusCommand : public Command {
21 RemoveOtusCommand(string);
23 ~RemoveOtusCommand(){}
25 vector<string> setParameters();
26 string getCommandName() { return "remove.otus"; }
27 string getCommandCategory() { return "OTU-Based Approaches"; }
29 string getHelpString();
30 string getOutputPattern(string);
31 string getCitation() { return "http://www.mothur.org/wiki/Remove.otus"; }
32 string getDescription() { return "outputs a new list file containing the otus NOT containing sequences from the groups specified"; }
35 void help() { m->mothurOut(getHelpString()); }
38 string accnosfile, groupfile, listfile, outputDir, groups, label;
40 vector<string> outputNames, Groups;
44 int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);