From: Kathryn Iverson <kd.iverson@gmail.com>
Date: Tue, 3 Jul 2012 16:47:57 +0000 (-0400)
Subject: updated parameters for kw
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=0469e54185b42ce6e22245718e5e35f35bd4bbb6

updated parameters for kw
---

diff --git a/kruskalwalliscommand.cpp b/kruskalwalliscommand.cpp
index dd5eb09..474e82c 100644
--- 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;