public:
SystemCommand(string);
- SystemCommand() { abort = true; calledHelp = true; }
+ SystemCommand() { setParameters(); abort = true; calledHelp = true; }
~SystemCommand(){}
- vector<string> setParameters() { return outputNames; } //dummy does not do anything
+ vector<string> setParameters();
string getCommandName() { return "system"; }
string getCommandCategory() { return "General"; }
- string getHelpString();
-
+ string getOutputFileNameTag(string, string) { return ""; }
+ 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()); }