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"
15 /**************************************************************************************************/
17 class SummaryTaxCommand : public Command {
19 SummaryTaxCommand(string);
21 ~SummaryTaxCommand(){}
23 vector<string> setParameters();
24 string getCommandName() { return "summary.tax"; }
25 string getCommandCategory() { return "Phylotype Analysis"; }
26 string getOutputFileNameTag(string, string);
27 string getHelpString();
28 string getCitation() { return "http://www.mothur.org/wiki/Summary.tax"; }
29 string getDescription() { return "summarize the taxonomies of a set of sequences"; }
32 void help() { m->mothurOut(getHelpString()); }
36 string taxfile, outputDir, namefile, groupfile, refTaxonomy;
37 vector<string> outputNames;
38 map<string, int> nameMap;
41 /**************************************************************************************************/