X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=getgroupcommand.cpp;h=ab3ccfa36f3f2d4e6a7e1f5af6a38434640f3105;hb=4f9a6e14a608172f8a97f0297a3b8e6ea267c518;hp=2847db149ac5e40defdbfdedfd9d99ae3df5d583;hpb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;p=mothur.git

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 2847db1..ab3ccfa 100644
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -24,8 +24,7 @@ vector<string> GetgroupCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetgroupCommand::GetgroupCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["bootgroup"] = tempOutNames;
 	}
@@ -61,10 +60,10 @@ vector<string> GetgroupCommand::getRequiredFiles(){
 GetgroupCommand::GetgroupCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -135,7 +134,7 @@ GetgroupCommand::~GetgroupCommand(){
 int GetgroupCommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 	
 		int num, inputData, count;
 		count = 0;