# HG changeset patch
# User bgruening
# Date 1450873722 18000
# Node ID 8ed7e3b6a16ca4a3bbec5b1e96305946035284de
# Parent  aaf01404686f1794eeea5d8b9870d703e92a6260
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

diff -r aaf01404686f -r 8ed7e3b6a16c deepTools_macros.xml
--- a/deepTools_macros.xml	Wed Dec 23 03:54:30 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 07:28:42 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 aaf01404686f -r 8ed7e3b6a16c plotHeatmap.xml
--- a/plotHeatmap.xml	Wed Dec 23 03:54:30 2015 -0500
+++ b/plotHeatmap.xml	Wed Dec 23 07:28:42 2015 -0500
@@ -32,7 +32,7 @@
                 #if $advancedOpt.sortRegions:
                     --sortRegions '$advancedOpt.sortRegions'
                 #end if
-          
+
                 #if $advancedOpt.sortUsing:
                     --sortUsing '$advancedOpt.sortUsing'
                 #end if
@@ -69,7 +69,7 @@
 
                 --whatToShow '$advancedOpt.whatToShow'
 
-                --startLabel '$advancedOpt.startLabel' 
+                --startLabel '$advancedOpt.startLabel'
                 --endLabel '$advancedOpt.endLabel'
                 --refPointLabel '$advancedOpt.referencePointLabel'
                 --regionsLabel '$advancedOpt.regionsLabel'
@@ -78,7 +78,7 @@
                     --plotTitle '$advancedOpt.plotTitle'
                 #end if
 
-                $advancedOpt.onePlotPerGroup
+                $advancedOpt.perGroup
 
                 @KMEANS_CLUSTERING@
 
@@ -113,7 +113,7 @@
                     <option value="std">std</option>
                 </param>
 
-                <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color" 
+                <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color"
                     help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
                     By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0).
                     Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
@@ -143,9 +143,7 @@
                     help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
                     <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
                     <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
-                    <option value="heatmap only">heatmap only</option>
                     <option value="heatmap and colorbar">heatmap and colorbar</option>
-                    <option value="colorbar only">colorbar only</option>
                 </param>
 
                 <param argument="--startLabel" type="text" value="TSS" size="10"
@@ -158,8 +156,8 @@
                 <param argument="--referencePointLabel" type="text" value="TSS" size="10"
                     label="Reference point label"
                     help ="Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc." />
-                <param argument="--regionsLabel" type="text" value="genes" size="30" 
-                    label="Labels for the regions plotted in the heatmap" 
+                <param argument="--regionsLabel" type="text" value="genes" size="30"
+                    label="Labels for the regions plotted in the heatmap"
                     help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, label1, label2.">
                     <sanitizer>
                         <valid initial="string.printable">
@@ -167,10 +165,12 @@
                     </sanitizer>
                 </param>
                 <expand macro="plotTitle" />
-                <param argument="--onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
-                    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."/>
+                <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
+                    label="Do one plot per group"
+                    help="When clustering is applied to the data, or the computematrix was performed on file containing
+                    groups separated by &quot;#&quot;, plot the groups next to each other. The default is to plot
+                    the samples next to each other. If this option is set, each group (or cluster) will get its own plot,
+                    with different samples stacked on top of each other."/>
 
                 <expand macro="kmeans_clustering" />
             </when>
@@ -199,19 +199,17 @@
 
 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
 Like profiler, it requires that computeMatrix was run first to calculate the values.
- 
-We implemented vast optional parameters to optimize the visual output and we encourage you to play around with the min/max values displayed in the heatmap as well as 
-with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of 
-groups with similar read distributions that you expect and the algorithm will do the sorting for you.
 
-Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows
+We implemented vast optional parameters to optimize the visual output and we encourage you to play around with the min/max values
+displayed in the heatmap as well as with the different coloring options. The most powerful option is the k-means/hirarchichal clustering
+where you simply need to indicate the number of groups with similar read distributions that you expect and the algorithm will do the sorting for you.
 
 
 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
    :alt: Heatmap of RNA Polymerase II ChIP-seq
 
 
-You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper
+You can find more details on the tool on the plotHeatmap doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/plotHeatmap.html
 
 
 -----
diff -r aaf01404686f -r 8ed7e3b6a16c static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r aaf01404686f -r 8ed7e3b6a16c test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r aaf01404686f -r 8ed7e3b6a16c test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r aaf01404686f -r 8ed7e3b6a16c test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Wed Dec 23 03:54:30 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 07:28:42 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 aaf01404686f -r 8ed7e3b6a16c test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r aaf01404686f -r 8ed7e3b6a16c test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed