# HG changeset patch
# User bgruening
# Date 1450873761 18000
# Node ID a259f484f8849426ea13fc132cc50da552cdb770
# Parent  1a9fad4988f3cde6ccfa159e141bf0e8bf5c264e
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

diff -r 1a9fad4988f3 -r a259f484f884 bamCoverage.xml
--- a/bamCoverage.xml	Wed Dec 23 03:55:11 2015 -0500
+++ b/bamCoverage.xml	Wed Dec 23 07:29:21 2015 -0500
@@ -43,9 +43,9 @@
                 @ADVANCED_OPTS_READ_PROCESSING@
                 $advancedOpt.skipNAs
 
-                if str($advancedOpt.ignoreForNormalization).strip() != '':
+                #if str($advancedOpt.ignoreForNormalization).strip() != '':
                     --ignoreForNormalization $advancedOpt.ignoreForNormalization
-                end if
+                #end if
             #end if
 ]]>
     </command>
@@ -54,7 +54,7 @@
         <param name="bamInput" format="bam" type="data" label="BAM file"
             help="The BAM file must be sorted."/>
 
-        <param name="binSize" type="integer" value="50" min="1" 
+        <param name="binSize" type="integer" value="50" min="1"
             label="Bin size in bp"
             help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads)  will be reported. If only half a fragment overlaps, this fraction will be reported. "/>
 
@@ -149,7 +149,7 @@
         <test>
             <param name="bamInput" value="phiX.bam" ftype="bam" />
             <param name="outFileFormat" value="bedgraph" />
-            <param name="showAdvancedOpt" value="no" />
+            <param name="showAdvancedOpt" value="yes" />
             <param name="binSize" value="10" />
             <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
         </test>
@@ -171,7 +171,7 @@
 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
 
 
-You can find more details on the bamCoverage wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage
+You can find more details on the bamCoverage doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/bamCoverage.html
 
 
 **Output files**:
diff -r 1a9fad4988f3 -r a259f484f884 deepTools_macros.xml
--- a/deepTools_macros.xml	Wed Dec 23 03:55:11 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 07:29:21 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 1a9fad4988f3 -r a259f484f884 static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r 1a9fad4988f3 -r a259f484f884 test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r 1a9fad4988f3 -r a259f484f884 test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r 1a9fad4988f3 -r a259f484f884 test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Wed Dec 23 03:55:11 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 07:29:21 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 1a9fad4988f3 -r a259f484f884 test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 1a9fad4988f3 -r a259f484f884 test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed