vector<string> setParameters();
string getCommandName() { return "set.dir"; }
string getCommandCategory() { return "General"; }
- string getHelpString();
+ string getHelpString();
+ string getOutputPattern(string){ return ""; }
+ string getCitation() { return "http://www.mothur.org/wiki/Set.dir"; }
+ string getDescription() { return "set input, output and default directories"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
CommandFactory* commandFactory;
string output, input, tempdefault;
- bool abort;
+ bool abort, debugOnly, modifyNames;
vector<string> outputNames;