Galaxy |

Changeset 3:eae52f5abf7b (2016-03-09)

Previous changeset 2:b15aaad44ab8 (2016-02-18) Next changeset 4:0193cb4d153c (2016-03-10)

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

modified:
deepTools_macros.xml
plotPCA.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 b15aaad44ab8 -r eae52f5abf7b deepTools_macros.xml
--- a/deepTools_macros.xml Thu Feb 18 11:52:11 2016 -0500
+++ b/deepTools_macros.xml Wed Mar 09 18:26:45 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 b15aaad44ab8 -r eae52f5abf7b plotPCA.xml
--- a/plotPCA.xml Thu Feb 18 11:52:11 2016 -0500
+++ b/plotPCA.xml Wed Mar 09 18:26:45 2016 -0500

[

@@ -12,15 +12,22 @@
             --plotTitle "$plotTitle"
             --plotFile "$outFileName"
             --plotFileFormat "$outFileFormat"
+            #if $outFileNameData
+                --outFileNameData "$output_outFileNameData"
+            #end if
]]>
     </command>
     <inputs>
         <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary or multiBigwigSummary tools"/>
         <expand macro="input_image_file_format" />
         <expand macro="plotTitle" />
+        <param argument="--outFileNameData" type="boolean" label="Save the matrix of PCA and eigenvalues underlying the plot."/>
     </inputs>
     <outputs>
         <expand macro="output_image_file_format_not_nested" />
+        <data format="tabular" name="output_outFileNameData" label="${tool.name} on ${on_string}: PCA matrix">
+            <filter>outFileNameData</filter>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -29,17 +36,25 @@
             <param name="outFileFormat" value="png" />
             <output name="outFileName" file="plotPCA_result1.png" ftpye="png" compare="sim_size" delta="4000" />
         </test>
+        <test>
+            <param name="corData" value="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" />
+            <param name="plotTitle" value="Test Plot" />
+            <param name="outFileFormat" value="png" />
+            <param name="outFileNameData" value="True" />
+            <output name="outFileName" file="plotPCA_result2.png" ftpye="png" compare="sim_size" delta="4000" />
+            <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" />
+        </test>
     </tests>
     <help>
<![CDATA[

What it does
----------------
+------------

-This tool takes the **default output file of ``multiBamSummary``** or ``multiBigwigSummary`` to perform a principal component analysis (PCA).
+This tool takes the **default output file** of ``multiBamSummary`` or ``multiBigwigSummary`` to perform a principal component analysis (PCA).

Output
--------------
+------

The result is a panel of two plots:

@@ -47,16 +62,16 @@
2. The **Scree plot** for the top five principal components where the bars represent the amount of variability explained by the individual factors and the red line traces the amount of variability is explained by the individual components in a cumulative manner

Example plot
----------------
+------------

.. image:: $PATH_TO_IMAGES/plotPCA_annotated.png
    :width: 600
    :height: 315

-===================
+-----

-Background
------------------
+Theoretical Background
+----------------------

Principal component analysis (PCA) can be used, for example, to determine whether **samples display greater variability** between experimental conditions than between replicates of the same treatment. PCA is also useful to identify unexpected patterns, such as those caused by batch effects or outliers.
Principal components represent the directions along which the variation in the data is maximal, so that the information (e.g., read coverage values) from thousands of regions can be represented by just a few dimensions.

diff -r b15aaad44ab8 -r eae52f5abf7b test-data/bamCoverage_result5.bw

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diff -r b15aaad44ab8 -r eae52f5abf7b test-data/computeMatrix_result1.gz

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diff -r b15aaad44ab8 -r eae52f5abf7b test-data/computeMatrix_result2.gz

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diff -r b15aaad44ab8 -r eae52f5abf7b test-data/computeMatrix_result3.gz

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diff -r b15aaad44ab8 -r eae52f5abf7b test-data/heatmapper_result1.png

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diff -r b15aaad44ab8 -r eae52f5abf7b test-data/heatmapper_result2.png

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diff -r b15aaad44ab8 -r eae52f5abf7b test-data/heatmapper_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/heatmapper_result2.tabular Wed Mar 09 18:26:45 2016 -0500

@@ -0,0 +1,3 @@
+bin labels -0.0Kb 0.0Kb
+bins 1 2
+file_0 genes 2477942.34473 2610259.65234

diff -r b15aaad44ab8 -r eae52f5abf7b test-data/plotCorrelation_result1.png

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diff -r b15aaad44ab8 -r eae52f5abf7b test-data/plotCoverage_result1.png

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diff -r b15aaad44ab8 -r eae52f5abf7b test-data/plotPCA_result1.png

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diff -r b15aaad44ab8 -r eae52f5abf7b test-data/plotPCA_result2.png

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diff -r b15aaad44ab8 -r eae52f5abf7b test-data/plotPCA_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotPCA_result2.tabular Wed Mar 09 18:26:45 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 b15aaad44ab8 -r eae52f5abf7b test-data/profiler_result1.png

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diff -r b15aaad44ab8 -r eae52f5abf7b test-data/profiler_result2.png

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diff -r b15aaad44ab8 -r eae52f5abf7b test-data/profiler_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/profiler_result2.tabular Wed Mar 09 18:26:45 2016 -0500

@@ -0,0 +1,3 @@
+bin labels -0.0Kb 0.0Kb
+bins 1 2
+file_0 genes 2477942.34473 2610259.65234