*/
#include "command.hpp"
+#include "counttable.h"
/**************************************************************************************************/
vector<string> setParameters();
string getCommandName() { return "summary.tax"; }
string getCommandCategory() { return "Phylotype Analysis"; }
- string getHelpString();
+
+ string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Summary.tax"; }
string getDescription() { return "summarize the taxonomies of a set of sequences"; }
void help() { m->mothurOut(getHelpString()); }
private:
- bool abort;
- string taxfile, outputDir, namefile, groupfile, refTaxonomy;
+ bool abort, relabund;
+ string taxfile, outputDir, namefile, groupfile, refTaxonomy, countfile;
vector<string> outputNames;
map<string, int> nameMap;
};
+/**************************************************************************************************/
+
+
#endif