--- a/heatmapper.xml	Mon Dec 16 15:13:08 2013 -0500
+++ b/heatmapper.xml	Sat Dec 21 14:26:06 2013 -0500
@@ -80,9 +80,11 @@
 
             $advancedOpt.onePlotPerGroup
 
-            #if $advancedOpt.clustering.clustering_options == 'kmeans':
-                #if int($advancedOpt.clustering.k_kmeans) > 0:
-                    --kmeans $advancedOpt.clustering.k_kmeans
+            #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'yes':
+                #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
+                    #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
+                        --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
+                    #end if
                 #end if
             #end if
 
@@ -156,23 +158,41 @@
                 <param name="endLabel" type="text" value="TES" size="10" label="Label for the region end" help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/>
 
                 <param name="referencePointLabel" type="text" value="TSS" size="10" label="Reference point label" help ="[only for scale-regions mode] Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc." />
-                <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
+                <param name="regionsLabel" type="text" value="genes" size="30" 
+                    label="Labels for the regions plotted in the heatmap" 
+                    help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, label1, label2.">
+                    <sanitizer>
+                        <valid initial="string.printable">
+                        </valid>
+                    </sanitizer>
+                </param>
                 <param name="plotTitle" type="text" value="" size="30" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." />
-                <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" help="When the region file contains groups separated by &quot;#&quot;, the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/>
+                <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" 
+                    label="Do one plot per group" 
+                    help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default. If this option is set, each group will get its own plot, stacked on top of each other."/>
 
-                <conditional name="clustering">
-                    <param name="clustering_options" type="select" label="Clustering algorithm">
-                        <option value="none">No clustering</option>
-                        <option value="kmeans">Kmeans clustering</option>
+                <conditional name="used_multiple_regions">
+                    <param name="used_multiple_regions_options" type="select" 
+                        label="Did you used multiple regions in ComputeMatrix?"
+                        help="That option is only relevant if you want to cluster the results. Clustering is only available with one selected region in ComputeMatrix.">
+                        <option value="no">No, I used only one region.</option>
+                        <option value="yes">Yes, I used multiple regions.</option>
                     </param>
-                    <when value="kmeans">
-                        <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" 
-                            help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
+                    <when value="yes">
+                        <conditional name="clustering">
+                            <param name="clustering_options" type="select" label="Clustering algorithm">
+                                <option value="none">No clustering</option>
+                                <option value="kmeans">Kmeans clustering</option>
+                            </param>
+                            <when value="kmeans">
+                                <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" 
+                                    help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
+                            </when>
+                            <when value="none" />
+                        </conditional>
                     </when>
-                    <when value="none" />
+                    <when value="no" />
                 </conditional>
-
-
             </when>
         </conditional>
     </inputs>