1 #ifndef REMOVERARECOMMAND_H
2 #define REMOVERARECOMMAND_H
8 * Created by westcott on 1/21/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
14 #include "command.hpp"
15 #include "listvector.hpp"
18 class RemoveRareCommand : public Command {
22 RemoveRareCommand(string);
24 ~RemoveRareCommand(){}
26 vector<string> setParameters();
27 string getCommandName() { return "remove.rare"; }
28 string getCommandCategory() { return "OTU-Based Approaches"; }
30 string getHelpString();
31 string getOutputPattern(string);
32 string getCitation() { return "http://www.mothur.org/wiki/Remove.rare"; }
33 string getDescription() { return "removes rare sequences from a sabund, rabund, shared or list and group file"; }
37 void help() { m->mothurOut(getHelpString()); }
40 string sabundfile, rabundfile, sharedfile, groupfile, countfile, listfile, outputDir, groups, label;
43 vector<string> outputNames, Groups;
50 int processLookup(vector<SharedRAbundVector*>&);