# HG changeset patch
# User bgruening
# Date 1450873566 18000
# Node ID b67afe81e29c4230739c084d14d809d0910a3c61
# Parent  d6ae9280ef213954f3baec2a2237c80fa6cf5963
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

diff -r d6ae9280ef21 -r b67afe81e29c bamCorrelate.xml
--- a/bamCorrelate.xml	Wed Dec 23 03:51:51 2015 -0500
+++ b/bamCorrelate.xml	Wed Dec 23 07:26:06 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 d6ae9280ef21 -r b67afe81e29c deepTools_macros.xml
--- a/deepTools_macros.xml	Wed Dec 23 03:51:51 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 07:26:06 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 d6ae9280ef21 -r b67afe81e29c static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r d6ae9280ef21 -r b67afe81e29c test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r d6ae9280ef21 -r b67afe81e29c test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r d6ae9280ef21 -r b67afe81e29c test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Wed Dec 23 03:51:51 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 07:26:06 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 d6ae9280ef21 -r b67afe81e29c test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r d6ae9280ef21 -r b67afe81e29c test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed