--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plotCorrelation.xml	Mon Jan 25 20:22:46 2016 -0500
@@ -0,0 +1,126 @@
+<tool id="deeptools_plot_correlation" name="plotCorrelation" version="@WRAPPER_VERSION@.0">
+    <description>creates a heatmap or scatterplot of correlation scores between different samples </description>
+    <macros>
+        <token name="@BINARY@">plotCorrelation</token>
+        <import>deepTools_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command>
+<![CDATA[
+        @BINARY@
+            --corData "$corData"
+            --plotFile "$outFileName"
+            --corMethod "$corMethod"
+            --whatToPlot "$plotting_type.whatToPlot"
+            #if str($plotting_type.whatToPlot) == 'heatmap':
+                @HEATMAP_OPTIONS@
+            #else:
+                --plotTitle '$plotting_type.plotTitle'
+            #end if
+            $skipZeros
+            --plotFileFormat "$outFileFormat"
+            $removeOutliers
+            #if $outFileCorMatrix:
+                --outFileCorMatrix "$matrix"
+            #end if
+
+]]>
+    </command>
+    <inputs>
+        <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary tool"/>
+        <expand macro="corMethod" />
+
+        <conditional name="plotting_type" >
+            <param argument="--whatToPlot" type="select" label="Plotting type">
+                <option value="heatmap" selected="True">Heatmap</option>
+                <option value="scatterplot">Scatterplot</option>
+            </param>
+            <when value="heatmap">
+                <expand macro="heatmap_options" />
+            </when>
+            <when value="scatterplot">
+                <expand macro="plotTitle" />
+            </when>
+        </conditional>
+
+        <expand macro="skipZeros" />
+
+        <expand macro="input_image_file_format" />
+
+        <param argument="--removeOutliers" type="boolean"
+            truevalue="--removeOutliers" falsevalue="" label="Remove regions with very large counts"
+            help="If set, bins with very large counts are removed. Bins
+                with abnormally high reads counts artificially
+                increase pearson correlation; that's why, by default,
+                plotCorrelation tries to remove outliers using the median
+                absolute deviation (MAD) method applying a threshold
+                of 200 to only consider extremely large deviations
+                from the median. ENCODE blacklist page (https://sites.
+                google.com/site/anshulkundaje/projects/blacklists)
+                contains useful information about regions with
+                unusually high counts."/>
+
+        <param name="outFileCorMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
+
+    </inputs>
+    <outputs>
+        <expand macro="output_image_file_format_not_nested" />
+        <data format="tabular" name="matrix" label="${tool.name} on ${on_string}: Correlation matrix">
+            <filter>outFileCorMatrix is True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
+            <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="100" />
+        </test>
+        <test>
+            <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
+            <param name="outFileFormat" value="png" />
+            <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="100" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**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
+a heatmap of correlation coefficients. Further output files are optional.
+The compressed input matrices are easily generated using the "multiBamSummary" and "multiBigwigSummary" tools.
+
+
+.. image:: $PATH_TO_IMAGES/QC_multiBamSummary_humanSamples.png
+   :alt: Heatmap of RNA Polymerase II ChIP-seq
+
+
+You can find more details on plotCorrelation here http://deeptools.readthedocs.org/en/master/content/tools/plotCorrelation.html
+
+
+**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
+- 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**:
+
+The 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 multiBigwigSummary. 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@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>