#include "systemcommand.h"
-
+//**********************************************************************************************************************
+vector<string> SystemCommand::setParameters(){
+ try {
+ CommandParameter pcommand("command", "String", "", "", "", "", "",false,false); parameters.push_back(pcommand);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SystemCommand", "setParameters");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
SystemCommand::SystemCommand(string option) {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- if (option == "") { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
- else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+ map<string, string>::iterator it;
+
+ ValidParameters validParameter;
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ string commandOption = validParameter.validFile(parameters, "command", false);
+ if (commandOption == "not found") { commandOption = ""; }
+ else { command = commandOption; }
+
+ if ((option == "") && (commandOption == "")) { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
+ else if (commandOption == "") {
//check for outputdir and inputdir parameters
int commaPos = option.find_first_of(',');