Galaxy |

Changeset 3:df65a17fb5d1 (2016-03-09)

Previous changeset 2:fcb4e6e95544 (2016-02-18) Next changeset 4:2b17c904ce2c (2016-03-10)

Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c

modified:
deepTools_macros.xml
plotCorrelation.xml
test-data/computeMatrix_result1.gz
test-data/computeMatrix_result2.gz
test-data/computeMatrix_result3.gz
test-data/heatmapper_result1.png
test-data/heatmapper_result2.png
test-data/plotCorrelation_result1.png
test-data/plotCoverage_result1.png
test-data/plotPCA_result1.png
test-data/profiler_result1.png
test-data/profiler_result2.png

added:
test-data/bamCoverage_result5.bw
test-data/heatmapper_result2.tabular
test-data/plotPCA_result2.png
test-data/plotPCA_result2.tabular
test-data/profiler_result2.tabular

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

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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