# HG changeset patch
# User bgruening
# Date 1391163161 18000
# Node ID ea2f64efe70dec03d2a0fdda28b587bf93d2981a
# Parent  7766dfcd2455f1e9924317122a13f4585340be57
Uploaded

diff -r 7766dfcd2455 -r ea2f64efe70d deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Jan 30 19:16:15 2014 -0500
+++ b/deepTools_macros.xml	Fri Jan 31 05:12:41 2014 -0500
@@ -56,6 +56,43 @@
         </requirements>
         <version_command>@BINARY@ --version</version_command>
     </xml>
+
+    <xml name="kmeans_clustering">
+
+        <conditional name="used_multiple_regions">
+            <param name="used_multiple_regions_options" type="select" 
+                label="Did you used multiple regions in ComputeMatrix?"
+                help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
+                <option value="yes">Yes, I used multiple regions.</option>
+                <option value="no">No, I used only one region.</option>
+            </param>
+            <when value="no">
+                <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="yes" />
+        </conditional>
+
+    </xml>
+    <token name="@kmeans_clusterin@">
+        #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
+            #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
+    </token>
+
     <xml name="stdio">
         <stdio>
             <exit_code range="1:" />
diff -r 7766dfcd2455 -r ea2f64efe70d heatmapper.xml
--- a/heatmapper.xml	Thu Jan 30 19:16:15 2014 -0500
+++ b/heatmapper.xml	Fri Jan 31 05:12:41 2014 -0500
@@ -81,13 +81,7 @@
 
             $advancedOpt.onePlotPerGroup
 
-            #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
-                #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
+            @kmeans_clusterin@
 
         #end if
     </command>
@@ -171,28 +165,8 @@
                     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="used_multiple_regions">
-                    <param name="used_multiple_regions_options" type="select" 
-                        label="Did you used multiple regions in ComputeMatrix?"
-                        help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
-                        <option value="yes">Yes, I used multiple regions.</option>
-                        <option value="no">No, I used only one region.</option>
-                    </param>
-                    <when value="no">
-                        <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="yes" />
-                </conditional>
+                <expand macro="kmeans_clustering" />
+
             </when>
         </conditional>
     </inputs>
diff -r 7766dfcd2455 -r ea2f64efe70d profiler.xml
--- a/profiler.xml	Thu Jan 30 19:16:15 2014 -0500
+++ b/profiler.xml	Fri Jan 31 05:12:41 2014 -0500
@@ -64,6 +64,9 @@
             #if str($advancedOpt.yAxisLabel.value) != "None":
                 --yAxisLabel '$advancedOpt.yAxisLabel'
             #end if
+
+            @kmeans_clusterin@
+
         #end if
     </command>
     <inputs>
@@ -123,6 +126,9 @@
                 <param name="yMax" type="float" value="" size="3" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
                 <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50" label="Description for the x-axis label" />
                 <param name="yAxisLabel" type="text" value="" size="50" label="Description for the y-axis label for the top panel" />
+
+                <expand macro="kmeans_clustering" />
+
             </when>
         </conditional>
     </inputs>