# HG changeset patch
# User bgruening
# Date 1457565603 18000
# Node ID df65a17fb5d16deaecf1e498e5b3d81866c2a6dd
# Parent  fcb4e6e95544d5274abe448494c3f3725847d7c9
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c

diff -r fcb4e6e95544 -r df65a17fb5d1 deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Feb 18 11:50:18 2016 -0500
+++ b/deepTools_macros.xml	Wed Mar 09 18:20:03 2016 -0500
@@ -72,12 +72,12 @@
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.1.0</token>
+    <token name="@WRAPPER_VERSION@">2.2.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
             <requirement type="binary">@BINARY@</requirement>
-            <requirement type="package" version="2.1.0">deepTools</requirement>
+            <requirement type="package" version="2.2.2">deepTools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -310,13 +310,13 @@
     <xml name="multiple_input_bams">
         <param argument="--bamfiles" type="data" format="bam" min="1"
             label="Bam file" multiple="true"
-            help="The BAM file must be sorted."/>
+            help=""/>
     </xml>
 
     <xml name="multiple_input_bams_min2">
         <param argument="--bamfiles" type="data" format="bam" min="2"
             label="Bam file" multiple="true"
-            help="The BAM file must be sorted."/>
+            help=""/>
     </xml>
 
     <xml name="multiple_input_bigwigs">
diff -r fcb4e6e95544 -r df65a17fb5d1 plotCorrelation.xml
--- a/plotCorrelation.xml	Thu Feb 18 11:50:18 2016 -0500
+++ b/plotCorrelation.xml	Wed Mar 09 18:20:03 2016 -0500
@@ -75,7 +75,7 @@
             <param name="outFileFormat" value="png" />
             <param name="outFileCorMatrix" value="True" />
             <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" />
-            <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="200" />
+            <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="300" />
         </test>
         <test>
             <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
@@ -83,20 +83,19 @@
             <param name="whatToPlot" value="scatterplot" />
             <param name="removeOutliers" value="True" />
             <param name="plotTitle" value="Test Plot" />
-            <output name="outFileName" file="plotCorrelation_result2.png" ftpye="png" compare="sim_size" delta="200" />
+            <output name="outFileName" file="plotCorrelation_result2.png" ftpye="png" compare="sim_size" delta="300" />
         </test>
     </tests>
     <help>
 <![CDATA[
 What it does
---------------
+------------
 
 This tools takes the default output of ``multiBamSummary`` or ``multiBigwigSummary``, and computes the pairwise correlation among samples.
-Results can be visualized as **scatterplots** or as
-a **heatmap** of correlation coefficients (see below for examples).
+Results can be visualized as **scatterplots** or as a **heatmap** of correlation coefficients (see below for examples).
 
-Background
-------------
+Theoretical Background
+----------------------
 
 The result of the correlation computation is a **table of correlation coefficients** that indicates how "strong" the relationship between two samples is and it will consist of numbers between -1 and 1. (-1 indicates perfect anti-correlation, 1 perfect correlation.)
 
@@ -106,18 +105,18 @@
 The *Spearman method* is based on **rankings**.
 
 Output
---------
+------
 
 The default output is a **diagnostic plot** -- either a scatterplot or a clustered heatmap displaying the values for each pair-wise correlation (see below for example plots).
 
 Optionally, you can also obtain a table of the pairwise correlation coefficients.
 
 .. image:: $PATH_TO_IMAGES/plotCorrelation_output.png
-   :width: 600
-   :height: 271
+    :width: 600
+    :height: 271
 
 Example plots
---------------
+-------------
 
 The following is the output of ``plotCorrelation`` with our test ChIP-Seq datasets (to be found under "Shared Data" --> "Data Library").
 
@@ -125,14 +124,14 @@
 from bigWig files using ``multiBigwigSummary``. This was then used with ``plotCorrelation`` to make a heatmap of Spearman correlation coefficients.
 
 .. image:: $PATH_TO_IMAGES/plotCorrelation_galaxy_bw_heatmap_output.png
-   :width: 600
-   :height: 518
+    :width: 600
+    :height: 518
 
 The scatterplot could look like this:
 
 .. image:: $PATH_TO_IMAGES/plotCorrelation_scatterplot_PearsonCorr_bigwigScores.png
-   :width: 600
-   :height: 600
+    :width: 600
+    :height: 600
 
 -----
 
diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/bamCoverage_result5.bw
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diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/computeMatrix_result1.gz
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diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/computeMatrix_result2.gz
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diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/computeMatrix_result3.gz
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diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/heatmapper_result1.png
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diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/heatmapper_result2.png
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diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/heatmapper_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/heatmapper_result2.tabular	Wed Mar 09 18:20:03 2016 -0500
@@ -0,0 +1,3 @@
+bin labels		-0.0Kb	0.0Kb
+bins		1	2
+file_0	genes	2477942.34473	2610259.65234
diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/plotCorrelation_result1.png
Binary file test-data/plotCorrelation_result1.png has changed
diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/plotCoverage_result1.png
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diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/plotPCA_result1.png
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diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/plotPCA_result2.png
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diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/plotPCA_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotPCA_result2.tabular	Wed Mar 09 18:20:03 2016 -0500
@@ -0,0 +1,3 @@
+Component	bowtie2-test1.bam	bowtie2-test1.bam	Eigenvalue
+1	-0.707106781187	-0.707106781187	6.0
+2	-0.707106781187	0.707106781187	1.23259516441e-32
diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/profiler_result1.png
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diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/profiler_result2.png
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diff -r fcb4e6e95544 -r df65a17fb5d1 test-data/profiler_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/profiler_result2.tabular	Wed Mar 09 18:20:03 2016 -0500
@@ -0,0 +1,3 @@
+bin labels		-0.0Kb	0.0Kb
+bins		1	2
+file_0	genes	2477942.34473	2610259.65234