1.21.0

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 6fccaba1381a22a618686b6f0bbd4c447026ca3e..905076b7dcd56b62102a3dbdbcef5de9024d0fef 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -38,7 +38,8 @@ vector<string> IndicatorCommand::setParameters(){
 string IndicatorCommand::getHelpString(){      
        try {
                string helpString = "";
-               helpString += "The indicator command reads a shared or relabund file and a tree or design file, and outputs a .indicator.tre and .indicator.summary file. \n";
+               helpString += "The indicator command can be run in 3 ways: with a shared or relabund file and a design file, or with a shared or relabund file and a tree file, or with a shared or relabund file, tree file and design file. \n";
+               helpString += "The indicator command outputs a .indicator.summary file and a .indicator.tre if a tree is given. \n";
                helpString += "The new tree contains labels at each internal node.  The label is the node number so you can relate the tree to the summary file.\n";
                helpString += "The summary file lists the indicator value for each OTU for each node.\n";
                helpString += "The indicator command parameters are tree, groups, shared, relabund, design and label. The tree parameter is required as well as either shared or relabund.\n";
@@ -229,7 +230,7 @@ int IndicatorCommand::execute(){
                
                int start = time(NULL);
        
-               //read designfile if given and set up globaldatas groups for read of sharedfiles
+               //read designfile if given and set up groups for read of sharedfiles
                if (designfile != "") {
                        designMap = new GroupMap(designfile);
                        designMap->readDesignMap();
@@ -256,7 +257,7 @@ int IndicatorCommand::execute(){
                        if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
                }
                
-               //reset Globaldatas groups if needed
+               //reset groups if needed
                if (designfile != "") { m->Groups = Groups; }
                        
                /***************************************************/