added [ERROR] flag if command aborts

[mothur.git] / systemcommand.cpp

diff --git a/systemcommand.cpp b/systemcommand.cpp
index fb250d7fe96cb4ed38df8c0ce33d1c7e17911945..abc07d0743a0a3e8f7172c27fe4094571abb3d5c 100644 (file)
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -46,10 +46,10 @@ vector<string> SystemCommand::getRequiredFiles(){
 
 SystemCommand::SystemCommand(string option)  {
        try {
-               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 (option == "") { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
@@ -92,7 +92,7 @@ void SystemCommand::help(){
 int SystemCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                system(command.c_str());