# HG changeset patch
# User bgruening
# Date 1450873878 18000
# Node ID b97024fb9c9f0d20d796b6cda09dae2e887c5d3e
# Parent  cb90587dfd3aa811c44215d6e7391f56575aa348
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

diff -r cb90587dfd3a -r b97024fb9c9f bamFingerprint.xml
--- a/bamFingerprint.xml	Wed Dec 23 03:57:06 2015 -0500
+++ b/bamFingerprint.xml	Wed Dec 23 07:31:18 2015 -0500
@@ -130,7 +130,7 @@
 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
 
 
-You can find more details on the bamFingerprint wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint
+You can find more details on the bamFingerprint doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/bamFingerprint.html
 
 
 **Output files**:
diff -r cb90587dfd3a -r b97024fb9c9f deepTools_macros.xml
--- a/deepTools_macros.xml	Wed Dec 23 03:57:06 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 07:31:18 2015 -0500
@@ -40,10 +40,10 @@
     </xml>
 
     <token name="@HEATMAP_OPTIONS@">
-        #if $plotting_type.zMin:
+        #if str($plotting_type.zMin) != "":
             --zMin $plotting_type.zMin
         #end if
-        #if $plotting_type.zMax:
+        #if str($plotting_type.zMax) != "":
             --zMax $plotting_type.zMax
         #end if
         --colorMap '$plotting_type.colorMap'
@@ -107,7 +107,11 @@
                     </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)."/>
+                            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: 0 [do not cluster])."/>
                     </when>
                     <when value="none" />
                 </conditional>
@@ -408,7 +412,6 @@
             <when value="no" />
             <when value="yes">
                 <yield />
-                <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
                 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
             </when>
         </conditional>
@@ -456,14 +459,6 @@
     </xml>
 
     <xml name="output_graphic_outputs">
-        <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
-            <filter>
-            ((
-                output['showOutputSettings'] == 'yes' and
-                output['saveData'] is True
-            ))
-            </filter>
-        </data>
         <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
             <filter>
             ((
diff -r cb90587dfd3a -r b97024fb9c9f static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r cb90587dfd3a -r b97024fb9c9f test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r cb90587dfd3a -r b97024fb9c9f test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r cb90587dfd3a -r b97024fb9c9f test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Wed Dec 23 03:57:06 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 07:31:18 2015 -0500
@@ -5,4 +5,4 @@
 chrM	220	230	7690304.31
 chrM	230	240	6027535.81
 chrM	240	250	3325537.00
-chrM	250	260	623538.19
+chrM	250	16569	623538.2
diff -r cb90587dfd3a -r b97024fb9c9f test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r cb90587dfd3a -r b97024fb9c9f test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed