updated parameters for kw

diff --git a/kruskalwalliscommand.cpp b/kruskalwalliscommand.cpp
index dd5eb09cbd3b54fb439d277cbd166f01dc726f84..474e82ced7a31ed287a2ecce360bc618c5746827 100644 (file)
--- a/kruskalwalliscommand.cpp
+++ b/kruskalwalliscommand.cpp
@@ -12,6 +12,8 @@ vector<string> KruskalWallisCommand::setParameters(){
        try {
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+        CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+        CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);    
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -91,8 +93,27 @@ KruskalWallisCommand::KruskalWallisCommand(string option) {
                        for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
-
-                       
+            
+            //get shared file
+                       sharedfile = validParameter.validFile(parameters, "shared", true);
+                       if (sharedfile == "not open") { sharedfile = ""; abort = true; }        
+                       else if (sharedfile == "not found") { 
+                               //if there is a current shared file, use it
+                               sharedfile = m->getSharedFile(); 
+                               if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+                               else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+                       }else { m->setSharedFile(sharedfile); }
+            
+            //if the user changes the output directory command factory will send this info to us in the output parameter 
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(sharedfile);             }
+                    
+            groups = validParameter.validFile(parameters, "groups", false);   
+            if (groups == "not found") { groups = "";   }
+            else { 
+            m->splitAtDash(groups, Groups); 
+            }   
+            m->setGroups(Groups);
+                               
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -127,7 +148,8 @@ int KruskalWallisCommand::execute(){
         InputData* input = new InputData(sharedfile, "sharedfile");
         vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
                string lastLabel = lookup[0]->getLabel();
-               
+        
+       
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> processedLabels;
                set<string> userLabels = labels;