added [ERROR] flag if command aborts

[mothur.git] / getlabelcommand.cpp

diff --git a/getlabelcommand.cpp b/getlabelcommand.cpp
index fe4387aa118487b5e60e120246b746222f93a5da..3191d5dda80670b8490203032e35170cf7642044 100644 (file)
--- a/getlabelcommand.cpp
+++ b/getlabelcommand.cpp
@@ -49,10 +49,10 @@ vector<string> GetlabelCommand::getRequiredFiles(){
 GetlabelCommand::GetlabelCommand(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 {
                        if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund or rabund before you can use the get.label command."); m->mothurOutEndLine(); abort = true; }                         
@@ -90,7 +90,7 @@ GetlabelCommand::~GetlabelCommand(){
 int GetlabelCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                filename = globaldata->inputFileName;
                ifstream in;