1 #ifndef COUNTGROUPSCOMMAND_H
2 #define COUNTGROUPSCOMMAND_H
8 * Created by westcott on 8/9/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
13 #include "command.hpp"
15 class CountGroupsCommand : public Command {
19 CountGroupsCommand(string);
21 ~CountGroupsCommand(){}
23 vector<string> setParameters();
24 string getCommandName() { return "count.groups"; }
25 string getCommandCategory() { return "Sequence Processing"; }
26 string getHelpString();
27 string getOutputPattern(string);
28 string getCitation() { return "http://www.mothur.org/wiki/Count.groups"; }
29 string getDescription() { return "counts the number of sequences in each group"; }
32 void help() { m->mothurOut(getHelpString()); }
36 string sharedfile, groupfile, countfile, outputDir, groups, accnosfile;
38 vector<string> Groups;
39 vector<string> outputNames;