diff --git a/coverage/src/test/java/Coverage/Coverage.java b/coverage/src/test/java/Coverage/Coverage.java
index 06d65d3a8..86f1b0ac8 100644
--- a/coverage/src/test/java/Coverage/Coverage.java
+++ b/coverage/src/test/java/Coverage/Coverage.java
@@ -1,4 +1,4 @@
-package coverage;
+package Coverage;
 
 import org.junit.jupiter.api.Test;
 
diff --git a/vip-application-importer/src/main/java/fr/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/DisplayTab.java b/vip-application-importer/src/main/java/fr/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/DisplayTab.java
index 6a6958fd7..b8490a287 100644
--- a/vip-application-importer/src/main/java/fr/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/DisplayTab.java
+++ b/vip-application-importer/src/main/java/fr/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/DisplayTab.java
@@ -170,11 +170,13 @@ private static void verifyBoutiquesTool(BoutiquesApplication boutiquesTool)
      * display warning message if any.
      *
      * @param application BoutiquesApplication object to cehck warning message 
+     * @throws ApplicationImporterException 
      * **/
-    private static void checkvipdot(BoutiquesApplication application) {
+    private static void checkvipdot(BoutiquesApplication application) throws ApplicationImporterException {
         Set<String> commandLineFlags = application.getCommandLineFlag();
         Set<String> vipDotInputIds = application.getVipDotInputIds();
-        Set<String> commonValues = new HashSet<>(application.getVipDotInputIds());
+        Set<String> inputIds = application.getinputIds();
+        Set<String> commonValues = new HashSet<>(vipDotInputIds);
         
         commonValues.retainAll(commandLineFlags);
 
@@ -182,15 +184,12 @@ private static void checkvipdot(BoutiquesApplication application) {
             String warningMessage = "<b>" + String.join(", ", commonValues) + "</b> appears as command-line flag input(s), it should not be included in Dot iteration. Importing it may cause functionality issues, although the application will still be imported.";
             Layout.getInstance().setWarningMessage(warningMessage);
         }
-
-        // Extract the IDs from inputs
-        Set<String> inputIds = application.getInputs().stream().map(BoutiquesInput::getId).collect(Collectors.toSet());
         // Check if all vipDotInputIds are in inputs
         if (!inputIds.containsAll(vipDotInputIds)) {
             Set<String> incorrectInputs = new HashSet<>(vipDotInputIds);
             incorrectInputs.removeAll(inputIds);
-            String warningMessage = "<b>" + String.join(", ", incorrectInputs) + "</b> appears in vipDotInputIds but not in inputs. Please ensure all ids are correct.";
-            Layout.getInstance().setWarningMessage(warningMessage);
+            String errorMessage = "<b>" + String.join(", ", incorrectInputs) + "</b> appears in vipDotInputIds but not in inputs. Please ensure all ids are correct.";
+            throw new ApplicationImporterException(errorMessage);
     }
     }
 
diff --git a/vip-application-importer/src/main/java/fr/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/GeneralLayout.java b/vip-application-importer/src/main/java/fr/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/GeneralLayout.java
index 441808528..22f44a5d9 100644
--- a/vip-application-importer/src/main/java/fr/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/GeneralLayout.java
+++ b/vip-application-importer/src/main/java/fr/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/GeneralLayout.java
@@ -78,6 +78,7 @@ public void setTool(BoutiquesApplication bt) {
         dockerIndex.setValue(bt.getContainerIndex());
         schemaVersion.setValue(bt.getSchemaVersion());
         vipContainer.setValue(bt.getVipContainer());
-        dotInputs.setValue(String.join(", ", bt.getVipDotInputIds()));
+        String dotInputsValue = String.join(", ", bt.getVipDotInputIds());
+        dotInputs.setValue(dotInputsValue + (bt.getVipDotIncludesResultsDir() ? (dotInputsValue.isEmpty() ? "results-directory" : ", results-directory") : ""));
     }
 }
diff --git a/vip-application/src/main/java/fr/insalyon/creatis/vip/application/client/bean/boutiquesTools/BoutiquesApplication.java b/vip-application/src/main/java/fr/insalyon/creatis/vip/application/client/bean/boutiquesTools/BoutiquesApplication.java
index 3325cc292..7ed6be189 100644
--- a/vip-application/src/main/java/fr/insalyon/creatis/vip/application/client/bean/boutiquesTools/BoutiquesApplication.java
+++ b/vip-application/src/main/java/fr/insalyon/creatis/vip/application/client/bean/boutiquesTools/BoutiquesApplication.java
@@ -42,7 +42,8 @@ public class BoutiquesApplication implements IsSerializable {
     private Map<String, String> tags = new HashMap<>();
     private String jsonFile;
     private Set<String> vipDotInputIds;
-    private String resultDirs;
+    private Set<String> inputIds;
+    private boolean vipDotIncludesResultsDir;
 
     private BoutiquesApplicationExtensions boutiquesExtensions;
 
@@ -248,8 +249,14 @@ public Set<String> getCommandLineFlag() {
                 .collect(Collectors.toSet());
     }
 
-    public String getVipDotResultDirs() {
-        return resultDirs;
+    public Set<String> getinputIds() {
+        return this.getInputs().stream()
+                .map(BoutiquesInput::getId)
+                .collect(Collectors.toSet());
+    }
+
+    public boolean getVipDotIncludesResultsDir() {
+        return vipDotIncludesResultsDir;
     }
 
     public void addInput(BoutiquesInput input){
@@ -308,7 +315,7 @@ public void setVipDotInputIds(Set<String> inputIds) {
         this.vipDotInputIds = inputIds;
     }
 
-    public void setVipDotResultDirs(String resultDirs) {
-        this.resultDirs = resultDirs;
+    public void setVipDotIncludesResultsDir(boolean vipDotIncludesResultsDir) {
+        this.vipDotIncludesResultsDir = vipDotIncludesResultsDir;
     }
 }
diff --git a/vip-application/src/main/java/fr/insalyon/creatis/vip/application/client/view/boutiquesParsing/BoutiquesParser.java b/vip-application/src/main/java/fr/insalyon/creatis/vip/application/client/view/boutiquesParsing/BoutiquesParser.java
index ef3ecbdbd..400d40956 100644
--- a/vip-application/src/main/java/fr/insalyon/creatis/vip/application/client/view/boutiquesParsing/BoutiquesParser.java
+++ b/vip-application/src/main/java/fr/insalyon/creatis/vip/application/client/view/boutiquesParsing/BoutiquesParser.java
@@ -116,7 +116,7 @@ public BoutiquesApplication parseApplication(String descriptor) throws InvalidBo
         if (customObject != null) {
             application.setVipContainer(getStringValue(customObject, "vip:imagepath", true));
             application.setVipDotInputIds(getArrayValueAsStringSet(customObject, "vip:dot", true));
-            application.setVipDotResultDirs(getStringValue(customObject, "vip:dot-result-directory", true));
+            application.setVipDotIncludesResultsDir(getBooleanValue(customObject, "vip:dot-with-results-directory", true));
         }
         // Json descriptor
         application.setJsonFile(parsedDescriptor.toString());
diff --git a/vip-portal/src/main/resources/vm/gwendia-standalone.vm b/vip-portal/src/main/resources/vm/gwendia-standalone.vm
index 36c49bbfa..e57a24789 100644
--- a/vip-portal/src/main/resources/vm/gwendia-standalone.vm
+++ b/vip-portal/src/main/resources/vm/gwendia-standalone.vm
@@ -5,112 +5,111 @@
     <source name="results-directory" type="URI" optional="false" default="/vip/Home" pretty-name="Results directory">
         <source-comment>Directory where the results will be stored.</source-comment>
     </source>
-    #foreach( $input in $tool.getInputs() )
-        #set($type="string")
-        #if($input.getType().getCamelName()=="File")
-            #set($type="URI")
-        #end
-        #if($input.getType().getCamelName()=="Flag")
-            #if($input.getDefaultValue() && $input.getDefaultValue()!="")
-                <source name="$input.getId()" type="string" optional="$input.isOptional()" default="$input.getDefaultValue()" vip-type-restriction="flag" pretty-name="$input.getName()">
-            #else
-                <source name="$input.getId()" type="string" optional="$input.isOptional()" default="false" vip-type-restriction="flag" pretty-name="$input.getName()">
-            #end
-        #else
-            #if($input.getDefaultValue() && $input.getDefaultValue()!="")
-                #if($input.getType().getCamelName()=="Number" && $input.isInteger())
-                    <source name="$input.getId()" type="$type" optional="$input.isOptional()" default="$input.getDefaultValue().intValue()" pretty-name="$input.getName()">
-                #else
-                    <source name="$input.getId()" type="$type" optional="$input.isOptional()" default="$input.getDefaultValue()" pretty-name="$input.getName()">
-                #end
-            #else
-                #if($input.isOptional()==true)
-                    <source name="$input.getId()" type="$type" optional="$input.isOptional()" default="No_value_provided" pretty-name="$input.getName()">
-                #else
-                    <source name="$input.getId()" type="$type" optional="$input.isOptional()" pretty-name="$input.getName()">
-                #end
-            #end
-        #end
-        #if($input.getDescription())
-            <source-comment>$esc.xml($input.getDescription())</source-comment>
-        #else
-            <source-comment></source-comment>
-        #end
-    </source>
+#foreach( $input in $tool.getInputs() )
+  #set($type="string")
+  #if($input.getType().getCamelName()=="File")
+    #set($type="URI")
+  #end
+  #if($input.getType().getCamelName()=="Flag")
+    #if($input.getDefaultValue() && $input.getDefaultValue()!="")
+      <source name="$input.getId()" type="string" optional="$input.isOptional()" default="$input.getDefaultValue()" vip-type-restriction="flag" pretty-name="$input.getName()">
+    #else
+      <source name="$input.getId()" type="string" optional="$input.isOptional()" default="false" vip-type-restriction="flag" pretty-name="$input.getName()">
     #end
-    #foreach($output in $tool.getOutputFiles())
-        <sink name="$output.getId()" type="URI" />
+  #else
+    #if($input.getDefaultValue() && $input.getDefaultValue()!="")
+       #if($input.getType().getCamelName()=="Number" && $input.isInteger())
+           <source name="$input.getId()" type="$type" optional="$input.isOptional()" default="$input.getDefaultValue().intValue()" pretty-name="$input.getName()">
+       #else
+           <source name="$input.getId()" type="$type" optional="$input.isOptional()" default="$input.getDefaultValue()" pretty-name="$input.getName()">
+       #end
+    #else
+      #if($input.isOptional()==true)
+    <source name="$input.getId()" type="$type" optional="$input.isOptional()" default="No_value_provided" pretty-name="$input.getName()">
+      #else
+    <source name="$input.getId()" type="$type" optional="$input.isOptional()" pretty-name="$input.getName()">
+      #end
     #end
+  #end
+  #if($input.getDescription())
+      <source-comment>$esc.xml($input.getDescription())</source-comment>
+  #else
+      <source-comment></source-comment>
+  #end
+    </source>
+#end
+#foreach($output in $tool.getOutputFiles())
+    <sink name="$output.getId()" type="URI" />
+#end
   </interface>
   <processors>
     <processor name="append-date" >
       <in name="dir" type="URI" depth="0" />
       <out name="result" type="string" depth="0" />
-      <beanshell>
-        /*----------Beginning of Beanshell------------*/
-        import java.text.DateFormat;
-        import java.text.SimpleDateFormat;
-        import java.util.Date;
+      <beanshell>/*----------Beginning of Beanshell------------*/
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.Date;
 
-        String result = dir.toString();
-        if ( result.startsWith("/") || result.startsWith("lfn:") ) {
-          DateFormat dateFormat = new SimpleDateFormat("dd-MM-yyyy_HH:mm:ss");
-          result = result + "/" + (dateFormat.format(System.currentTimeMillis()));
-        }
-        /*------------End of Beanshell------------*/
+String result = dir.toString();
+if ( result.startsWith("/") || result.startsWith("lfn:") ) {
+  DateFormat dateFormat = new SimpleDateFormat("dd-MM-yyyy_HH:mm:ss");
+  result = result + "/" + (dateFormat.format(System.currentTimeMillis()));
+}
+/*------------End of Beanshell------------*/
       </beanshell>
     </processor>
     <processor name="$tool.getName()" >
         <in name="results-directory" type="string" depth="0"/>
-        #foreach($input in $tool.getInputs())
-            #if($input.getType().getCamelName()=="File" )
-                <in name="$input.getId()" type="URI" depth="0"/>
-            #else
-                <in name="$input.getId()" type="string" depth="0"/>
-            #end
-        #end
-        #foreach( $output in $tool.getOutputFiles() )
-            <out name="$output.getId()" type="URI" depth="0"/>
-        #end
-        <iterationstrategy>
-          <cross>
-            #if($tools.getVipDotResultDirs)
-                <dot>
-                    <port name="results-directory" />
-                    #foreach($input in $tool.getInputs()) 
-                        #if($tool.getVipDotInputIds().contains($input.getId()))
-                            <port name="$input.getId()"/>
-                        #end
-                    #end
-                </dot>
-            #else
-                <port name="results-directory" />
-                #foreach($input in $tool.getInputs()) 
-                    #if(!$tool.getVipDotInputIds().contains($input.getId()))
-                        <port name="$input.getId()"/>
-                    #end
-                #end
-            #end
-            #if($tool.getVipDotInputIds() && !$tool.getVipDotInputIds().isEmpty() && !$tools.getVipDotResultDirs)
-                <dot>
-                    #foreach($dotInput in $tool.getVipDotInputIds())
-                        <port name="$dotInput"/>
-                    #end
-                </dot>
-            #end
-          </cross>
-        </iterationstrategy>
+#foreach($input in $tool.getInputs())
+  #if($input.getType().getCamelName()=="File" )
+        <in name="$input.getId()" type="URI" depth="0"/>
+  #else
+        <in name="$input.getId()" type="string" depth="0"/>
+  #end
+#end
+#foreach( $output in $tool.getOutputFiles() )
+        <out name="$output.getId()" type="URI" depth="0"/>
+#end
+      <iterationstrategy>
+        <cross>
+#if($tools.getVipDotResultDirs)
+          <dot>
+            <port name="results-directory" />
+#foreach($input in $tool.getInputs()) 
+  #if($tool.getVipDotInputIds().contains($input.getId()))
+            <port name="$input.getId()"/>
+  #end
+#end
+          </dot>
+#else
+          <port name="results-directory" />
+#foreach($input in $tool.getInputs()) 
+  #if(!$tool.getVipDotInputIds().contains($input.getId()))
+            <port name="$input.getId()"/>
+  #end
+#end
+#end
+#if($tool.getVipDotInputIds() && !$tool.getVipDotInputIds().isEmpty() && !$tools.getVipDotResultDirs)
+          <dot>
+#foreach($dotInput in $tool.getVipDotInputIds())
+            <port name="$dotInput"/>
+#end
+          </dot>
+#end
+        </cross>
+      </iterationstrategy>
         <gasw descriptor="$fileAccessProtocol:$tool.getGASWLFN()"/>
     </processor>
   </processors>
   <links>
     <link from="results-directory" to="append-date:dir" />
     <link from="append-date:result" to="$tool.getName():results-directory" />
-    #foreach( $input in $tool.getInputs() )
-        <link from="$input.getId()" to="$tool.getName():$input.getId()" />
-    #end
-    #foreach($output in $tool.getOutputFiles())
-        <link from="$tool.getName():$output.getId()" to="$output.getId()" />
-    #end
+#foreach( $input in $tool.getInputs() )
+    <link from="$input.getId()" to="$tool.getName():$input.getId()" />
+#end
+#foreach($output in $tool.getOutputFiles())
+    <link from="$tool.getName():$output.getId()" to="$output.getId()" />
+#end
   </links>
-</workflow>
+</workflow>
\ No newline at end of file