1 #ifndef SUMMARYTAXCOMMAND_H
2 #define SUMMARYTAXCOMMAND_H
8 * Created by westcott on 9/23/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "counttable.h"
16 /**************************************************************************************************/
18 class SummaryTaxCommand : public Command {
20 SummaryTaxCommand(string);
22 ~SummaryTaxCommand(){}
24 vector<string> setParameters();
25 string getCommandName() { return "summary.tax"; }
26 string getCommandCategory() { return "Phylotype Analysis"; }
27 string getOutputFileNameTag(string, string);
28 string getHelpString();
29 string getCitation() { return "http://www.mothur.org/wiki/Summary.tax"; }
30 string getDescription() { return "summarize the taxonomies of a set of sequences"; }
33 void help() { m->mothurOut(getHelpString()); }
37 string taxfile, outputDir, namefile, groupfile, refTaxonomy, countfile;
38 vector<string> outputNames;
39 map<string, int> nameMap;
42 /**************************************************************************************************/