--- a/masigpro.xml	Thu Jun 01 11:10:22 2017 -0400
+++ b/masigpro.xml	Thu Jul 13 18:23:17 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="masigpro" name="maSigPro" version="1.49.3.0">
+<tool id="masigpro" name="maSigPro" version="1.49.3.1">
     <description>Significant Gene Expression Profile Differences in Time Course Gene Expression Data</description>
     <requirements>
         <requirement type="package" version="1.49.3">bioconductor-masigpro</requirement>
@@ -70,6 +70,7 @@
     #if $pdf.pdf_selector:
         --cluster_data $pdf.seeGenes.clusterData
         -k $pdf.seeGenes.k
+        --print_cluster $pdf.seeGenes.print_cluster
         --cluster_method $pdf.seeGenes.clustering.clusterMethod
         #if str($pdf.seeGenes.clustering.clusterMethod) == "hclust":
             --distance $pdf.seeGenes.clustering.distance
@@ -277,6 +278,9 @@
                             ‘c(sig.profiles,coefficients,t.score)’ of their list
                             position (1,2 or 3)." />
                     <param name="k" type="integer" label="Number of clusters for data partioning" value="9" />
+                    <param name="print_cluster" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true"
+                        label="Add cluster information to summary file?"
+                        help="Adds columns with the cluster assignment for each gene." />
                     <conditional name="clustering">
                         <param name="clusterMethod" label="Cluster Method" type="select"
                             help="clustering method for data partioning. Currently
@@ -313,6 +317,8 @@
                             <param name="iterMax" type="integer" label="Maximum number of iterations" value="500"
                                 help="Maximum number of iterations when ‘cluster.method’ is ‘kmeans’" />
                         </when>
+                        <when value="Mclust">
+                        </when>
                     </conditional>
                     <param name="colorMode" label="Color Mode" type="select" help="Color scale for plotting profiles. Can be either ‘rainbow’ or ‘gray’">
                         <option selected="True" value="rainbow">Rainbow</option>
@@ -328,10 +334,18 @@
                         help="Indicating whether legend must be added when plotting profiles" />
                 </section>
             </when>
+            <when value="0">
+            </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format="tabular" name="masigpro_out" label="maSigPro result file on ${on_string}">
+        <data format="txt" name="data_out" label="maSigPro data file on ${on_string}">
+            <filter>
+                ((
+                    source['source_selector'] == 'advanced' and
+                    source['enable_output'] == True
+                ))
+            </filter>
         </data>
         <data format="txt" name="edesign_out" label="maSigPro edesign file on ${on_string}">
             <filter>
@@ -341,14 +355,6 @@
                 ))
             </filter>
         </data>
-        <data format="txt" name="data_out" label="maSigPro data file on ${on_string}">
-            <filter>
-                ((
-                    source['source_selector'] == 'advanced' and
-                    source['enable_output'] == True
-                ))
-            </filter>
-        </data>
         <data format="pdf" name="pdf_out" from_work_dir="Results.pdf" label="maSigPro Plot file on ${on_string}">
             <filter>
                 ((
@@ -356,6 +362,8 @@
                 ))
             </filter>
         </data>
+        <data format="tabular" name="masigpro_out" label="maSigPro result file on ${on_string}">
+        </data>
     </outputs>
     <tests>
         <test>
@@ -397,6 +405,14 @@
             <output name="masigpro_out" file="masigpro_out.tab" />
             <output name="pdf_out" file="Results.pdf" />
         </test>
+        <test>
+            <param name="source_selector" value="defaults" />
+            <param name="edesign" value="edesign_out.txt" />
+            <param name="data" value="data_out.txt" />
+            <param name="print_cluster" value="FALSE" />
+            <output name="masigpro_out" file="masigpro_out_no_cluster.tab" />
+            <output name="pdf_out" file="Results.pdf" />
+        </test>
     </tests>
     <help>
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