# HG changeset patch
# User bgruening
# Date 1450809542 18000
# Node ID 49cbd7e6ab07fd3677aeeb405926b4cd65dd6f97
# Parent  7a3698e9d4391bc1886da98ad33b358fced55dc2
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 8b9cdb8dc4a8fedd2b2286e7afab6529e49a9d22-dirty

diff -r 7a3698e9d439 -r 49cbd7e6ab07 bamCorrelate.xml
--- a/bamCorrelate.xml	Mon Dec 21 19:00:27 2015 -0500
+++ b/bamCorrelate.xml	Tue Dec 22 13:39:02 2015 -0500
@@ -20,7 +20,7 @@
             --labels '#echo "' '".join($labels)#'
 
             #if $outRawCounts:
-                --outRawCounts '$outFileRawCounts' 
+                --outRawCounts '$outFileRawCounts'
             #end if
 
             #if $mode.modeOpt == "bins":
@@ -45,16 +45,16 @@
 
         <conditional name="mode">
             <param name="modeOpt" type="select" label="Choose computation mode" 
-                    help="In the bins mode, the correlation is computed based on equal
+                    help="In the bins mode, the coverage is computed for equal
                     length bins. In the BED file mode, as list of genomic regions in BED
                     format has to be given. For each region in the BED file the number of
                     overlapping reads is counted in each of the BAM files.
-                    Then the correlation is computed.">
+                    ">
                 <option value="bins" selected="true">Bins</option>
-                <option value="BED-file">Limit correlation to certain regions (BED file)</option>
+                <option value="BED-file">Limit calculation to certain regions (BED file)</option>
             </param>
             <when value="bins">
-                <param name="binSize" type="integer" value="10000" min="1" 
+                <param name="binSize" type="integer" value="10000" min="1"
                     label="Bin size in bp"
                     help="Length in base pairs for a window used to sample the genome. (--binSize)"/>
 
@@ -64,7 +64,7 @@
             <when value="BED-file">
                 <param name="region_file" type="data" format="bed"
                     label="Region file in BED format"
-                    help="Correlation is computed for the number of reads that overlap such regions."/>
+                    help="Coverage is computed for the number of reads that overlap such regions."/>
             </when>
         </conditional>
 
@@ -113,7 +113,15 @@
 **Output files**:
 
 - **score matrix**: a compressed matrix where every row correponds to a genome region (or bin) and each column corresponds to a sample (BAM file)
-- optional: uncompressed **score matrix** for 
+- Optional : Uncompressed **score matrix**, in case you want to analyse the coverage scores yourself. (Select to "Save raw counts" from above)
+
+=======
+
+.. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png
+   :alt: Heatmap of RNA Polymerase II ChIP-seq
+
+
+You can find more details on the bamCorrelate doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/bamCorrelate.html
 
 -----
 
diff -r 7a3698e9d439 -r 49cbd7e6ab07 deepTools_macros.xml
--- a/deepTools_macros.xml	Mon Dec 21 19:00:27 2015 -0500
+++ b/deepTools_macros.xml	Tue Dec 22 13:39:02 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 7a3698e9d439 -r 49cbd7e6ab07 static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed