fixed mpi version compile issue with chimera.slayer

[mothur.git] / getgroupscommand.cpp

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index 1832f96aed8122020b5ddf0ad5881275e3cc6481..2d7ac5481dedbc90863bc58eb6035176d629d70e 100644 (file)
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -27,8 +27,7 @@ vector<string> GetGroupsCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetGroupsCommand::GetGroupsCommand(){  
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
                outputTypes["taxonomy"] = tempOutNames;
@@ -67,10 +66,10 @@ vector<string> GetGroupsCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 GetGroupsCommand::GetGroupsCommand(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 {
                        //valid paramters for this command
@@ -207,8 +206,8 @@ void GetGroupsCommand::help(){
                m->mothurOut("You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n");
                m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like.  You can separate group names with dashes.\n");
                m->mothurOut("The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n");
-               m->mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n");
-               m->mothurOut("or get.seqs(groups=pasture, fasta=amazon.fasta, amazon.groups).\n");
+               m->mothurOut("Example get.groups(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n");
+               m->mothurOut("or get.groups(groups=pasture, fasta=amazon.fasta, group=amazon.groups).\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
        }
        catch(exception& e) {
@@ -222,7 +221,7 @@ void GetGroupsCommand::help(){
 int GetGroupsCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                groupMap = new GroupMap(groupfile);
                groupMap->readMap();