public:
SystemCommand(string);
- SystemCommand() { abort = true; calledHelp = true; }
+ SystemCommand() { setParameters(); abort = true; calledHelp = true; }
~SystemCommand(){}
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
-
+
+ vector<string> setParameters();
+ string getCommandName() { return "system"; }
+ string getCommandCategory() { return "General"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/System"; }
+ string getDescription() { return "execute system commands from within mothur"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
string command;
bool abort;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
+
};