# HG changeset patch
# User bgruening
# Date 1450861065 18000
# Node ID 7cbaaf80dcedb676f0383d1073439f07b3ee6447
# Parent  ae54e08b15d7639b8de3f6271a9b07afb293c845
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41

diff -r ae54e08b15d7 -r 7cbaaf80dced deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Dec 22 13:45:00 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 03:57:45 2015 -0500
@@ -40,10 +40,10 @@
     </xml>
 
     <token name="@HEATMAP_OPTIONS@">
-        #if str($plotting_type.zMin) != "":
+        #if $plotting_type.zMin:
             --zMin $plotting_type.zMin
         #end if
-        #if str($plotting_type.zMax) != "":
+        #if $plotting_type.zMax:
             --zMax $plotting_type.zMax
         #end if
         --colorMap '$plotting_type.colorMap'
@@ -107,11 +107,7 @@
                     </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: 0 [do not cluster])."/>
+                            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)."/>
                     </when>
                     <when value="none" />
                 </conditional>
@@ -412,6 +408,7 @@
             <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>
@@ -459,6 +456,14 @@
     </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 ae54e08b15d7 -r 7cbaaf80dced plotCorrelation.xml
--- a/plotCorrelation.xml	Tue Dec 22 13:45:00 2015 -0500
+++ b/plotCorrelation.xml	Wed Dec 23 03:57:45 2015 -0500
@@ -1,5 +1,5 @@
 <tool id="deeptools_plot_correlation" name="plotCorrelation" version="@WRAPPER_VERSION@.0">
-    <description>creates a heatmap or scatterplot of correlation scores between different samples </description>
+    <description>creates a heatmap 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.
 
@@ -105,18 +105,10 @@
 
 **Output files**:
 
-- **diagnostic plot**: Either a scatterplot or clustered heatmap (select above) displaying the values for each pair-wise correlation,
-  see below for an example
+- **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
 - 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 ae54e08b15d7 -r 7cbaaf80dced static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r ae54e08b15d7 -r 7cbaaf80dced test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r ae54e08b15d7 -r 7cbaaf80dced test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r ae54e08b15d7 -r 7cbaaf80dced test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Tue Dec 22 13:45:00 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 03:57:45 2015 -0500
@@ -5,4 +5,4 @@
 chrM	220	230	7690304.31
 chrM	230	240	6027535.81
 chrM	240	250	3325537.00
-chrM	250	16569	623538.2
+chrM	250	260	623538.19
diff -r ae54e08b15d7 -r 7cbaaf80dced test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r ae54e08b15d7 -r 7cbaaf80dced test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed
diff -r ae54e08b15d7 -r 7cbaaf80dced tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Dec 22 13:45:00 2015 -0500
+++ b/tool_dependencies.xml	Wed Dec 23 03:57:45 2015 -0500
@@ -4,6 +4,6 @@
         <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="deepTools" version="2.0">
-        <repository changeset_revision="747571992679" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="bd40c0aa7d8e" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>