virtual string getCommandName() = 0;
virtual string getCommandCategory() = 0;
virtual string getHelpString() = 0;
+ virtual string getCitation() = 0;
virtual map<string, vector<string> > getOutputFiles() { return outputTypes; }
virtual vector<string> setParameters() = 0; //to fill parameters
virtual int execute() = 0;
virtual void help() = 0;
+ void citation() { m->mothurOut(getCitation()); }
virtual ~Command() { }
protected: