mods to trim.seqs

[mothur.git] / mergegroupscommand.cpp

diff --git a/mergegroupscommand.cpp b/mergegroupscommand.cpp
index ad0dc312361c0a5d55a35b919b0102832eabc858..c54cd1c7dd8e578126b345c68ac0ac1d8f684e19 100644 (file)
--- a/mergegroupscommand.cpp
+++ b/mergegroupscommand.cpp
@@ -25,8 +25,7 @@ vector<string> MergeGroupsCommand::getValidParameters(){
 //**********************************************************************************************************************
 MergeGroupsCommand::MergeGroupsCommand(){      
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["shared"] = tempOutNames;
        }
@@ -64,12 +63,12 @@ vector<string> MergeGroupsCommand::getRequiredFiles(){
 MergeGroupsCommand::MergeGroupsCommand(string option) {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                labels.clear();
                
                //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
@@ -153,14 +152,14 @@ MergeGroupsCommand::MergeGroupsCommand(string option) {
 void MergeGroupsCommand::help(){
        try {
                m->mothurOut("The merge.groups command reads a shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file.\n");
-               m->mothurOut("The metastats command outputs a .shared file. \n");
-               m->mothurOut("The metastats command parameters are shared, groups, label and design.  The design and shared parameter are required.\n");
+               m->mothurOut("The merge.groups command outputs a .shared file. \n");
+               m->mothurOut("The merge.groups command parameters are shared, groups, label and design.  The design and shared parameter are required.\n");
                m->mothurOut("The design parameter allows you to assign your groups to sets when you are running metastat. mothur will run all pairwise comparisons of the sets. It is required. \n");
                m->mothurOut("The design file looks like the group file.  It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.\n");
                m->mothurOut("The groups parameter allows you to specify which of the groups in your shared you would like included. The group names are separated by dashes.\n");
                m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
-               m->mothurOut("The merge.groups command should be in the following format: metastats(design=yourDesignFile, shared=yourSharedFile).\n");
-               m->mothurOut("Example metastats(design=temp.design, groups=A-B-C, shared=temp.shared).\n");
+               m->mothurOut("The merge.groups command should be in the following format: merge.groups(design=yourDesignFile, shared=yourSharedFile).\n");
+               m->mothurOut("Example merge.groups(design=temp.design, groups=A-B-C, shared=temp.shared).\n");
                m->mothurOut("The default value for groups is all the groups in your sharedfile, and all labels in your inputfile will be used.\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
                
@@ -180,7 +179,7 @@ MergeGroupsCommand::~MergeGroupsCommand(){}
 int MergeGroupsCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                if (outputDir == "") {  outputDir += m->hasPath(sharedfile);  }
                string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "merge" +  m->getExtension(sharedfile);