fixed bug in phylo.diversity rooting. added filename patterns and create filename...

[mothur.git] / countgroupscommand.cpp

diff --git a/countgroupscommand.cpp b/countgroupscommand.cpp
index 716dc90693969140d3af32403d3818c04224d7f9..215c2e5a24c925e449ecbb297f267c463f283d39 100644 (file)
--- a/countgroupscommand.cpp
+++ b/countgroupscommand.cpp
@@ -14,13 +14,13 @@
 //**********************************************************************************************************************
 vector<string> CountGroupsCommand::setParameters(){    
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pshared);
-               CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pgroup);
-        CommandParameter pcount("count", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pcount);
-               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pshared("shared", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","",false,false,true); parameters.push_back(pshared);
+               CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","",false,false,true); parameters.push_back(pgroup);
+        CommandParameter pcount("count", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","",false,false,true); parameters.push_back(pcount);
+               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }