added out.hierarchy command

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 4254950ba8560efe2b8714b77f8905228ce8d92e..e68890cec67c253ae78e9400f865b4b66739a07b 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -103,7 +103,7 @@ CollectSharedCommand::CollectSharedCommand(string option){
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
                        convert(temp, freq); 
                        
-                       temp = validParameter.validFile(parameters, "all", false);                              if (temp == "not found") { temp = "true"; }
+                       temp = validParameter.validFile(parameters, "all", false);                              if (temp == "not found") { temp = "false"; }
                        all = isTrue(temp);
                                                
                        if (abort == false) {
@@ -184,7 +184,7 @@ void CollectSharedCommand::help(){
                mothurOut("The default value for groups is all the groups in your groupfile.\n");
                validCalculator->printCalc("shared", cout);
                mothurOut("The label parameter is used to analyze specific labels in your input.\n");
-               mothurOut("The all parameter is used to specify if you want the estimate of all your groups together.  This estimate can only be made for sharedsobs and sharedchao calculators. The default is true.\n");
+               mothurOut("The all parameter is used to specify if you want the estimate of all your groups together.  This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n");
                mothurOut("If you use sharedchao and run into memory issues, set all to false. \n");
                mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n");
                mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");