# HG changeset patch
# User bgruening
# Date 1450873918 18000
# Node ID 44d87fb8403e96a4815ae4652241288a7e74ea7d
# Parent  7cbaaf80dcedb676f0383d1073439f07b3ee6447
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

diff -r 7cbaaf80dced -r 44d87fb8403e deepTools_macros.xml
--- a/deepTools_macros.xml	Wed Dec 23 03:57:45 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 07:31:58 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 7cbaaf80dced -r 44d87fb8403e plotCorrelation.xml
--- a/plotCorrelation.xml	Wed Dec 23 03:57:45 2015 -0500
+++ b/plotCorrelation.xml	Wed Dec 23 07:31:58 2015 -0500
@@ -1,5 +1,5 @@
 <tool id="deeptools_plot_correlation" name="plotCorrelation" version="@WRAPPER_VERSION@.0">
-    <description>creates a heatmap of correlation scores between different samples </description>
+    <description>creates a heatmap or scatterplot of correlation scores between different samples </description>
     <macros>
         <token name="@BINARY@">plotCorrelation</token>
         <import>deepTools_macros.xml</import>
@@ -91,7 +91,7 @@
 **What it does**
 
 This tools takes a compressed matrix of scores (such as read coverages) for a number of genomic regions
-and different samples. It can visualize the correlation among samples as scatterplots or as 
+and different samples. It can visualize the correlation among samples as scatterplots or as
 heatmap of correlation coefficients. Further output files are optional.
 The compressed input matrices are easily generated using the "bamCorrelate" and "bigwigCorrelate" modules of deeptools.
 
@@ -105,10 +105,18 @@
 
 **Output files**:
 
-- **correlation structure**: a scatterplot of all mutual correlations between all samples in matrix
-- **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation, see below for an example
+- **diagnostic plot**: Either a scatterplot or clustered heatmap (select above) displaying the values for each pair-wise correlation,
+  see below for an example
 - data matrix (optional): if you want to analyze or plot the correlation values using a different program, e.g. R, this matrix can be used
 
+**Output with test dataset**:
+
+Following is the output of plotCorrelation with our test ChIP-Seq datasets. Average coverages were computed over 10kb bins for chromosome X,
+from bigwig files using bigwigCorrelate. The output was used by plotCorrelation to make a heatmap of spearman correlation between samples.
+
+.. image:: $PATH_TO_IMAGES/plotCorrelation_galaxy_bw_heatmap_output.png
+
+
 -----
 
 @REFERENCES@
diff -r 7cbaaf80dced -r 44d87fb8403e static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r 7cbaaf80dced -r 44d87fb8403e test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r 7cbaaf80dced -r 44d87fb8403e test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r 7cbaaf80dced -r 44d87fb8403e test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Wed Dec 23 03:57:45 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 07:31:58 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 7cbaaf80dced -r 44d87fb8403e test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 7cbaaf80dced -r 44d87fb8403e test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed