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[mothur.git] / pipelinepdscommand.cpp

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index b7ba7d382476ade9782660f4b9127c9c1b55b513..84282dcc39105c7f4d560b88fcacdcb4ed4342d6 100644 (file)
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -49,10 +49,10 @@ vector<string> PipelineCommand::getRequiredFiles(){
 PipelineCommand::PipelineCommand(string option) {
        try {
                cFactory = CommandFactory::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 {
                        
@@ -235,7 +235,7 @@ PipelineCommand::~PipelineCommand(){}
 
 int PipelineCommand::execute(){
        try {
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                int start = time(NULL);
                
@@ -525,6 +525,8 @@ int PipelineCommand::runUsersPipeline(){
                }
                
                in.close();
+               
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "PipelineCommand", "runUsersPipeline");