--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/multiBigwigSummary.xml	Mon Jan 25 20:19:55 2016 -0500
@@ -0,0 +1,118 @@
+<tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.0">
+    <description>calculates average read coverages for a list of two or more bigwig files</description>
+    <macros>
+        <token name="@BINARY@">multiBigwigSummary</token>
+        <import>deepTools_macros.xml</import>
+    </macros>
+   <expand macro="requirements" />
+    <command>
+<![CDATA[
+        #set files=[]
+        #set labels=[]
+
+        @multiple_input_bigwigs@
+
+        @BINARY@
+            $mode.modeOpt
+
+            @THREADS@
+
+            --outFileName $outFile
+            --bwfiles '#echo "' '".join($files)#'
+            --labels '#echo "' '".join($labels)#'
+
+            #if $outRawCounts:
+                --outRawCounts '$outFileRawCounts'
+            #end if
+
+            #if $mode.modeOpt == "bins":
+                --binSize '$mode.binSize'
+                --distanceBetweenBins '$mode.distanceBetweenBins'
+            #else:
+                --BED $mode.region_file
+            #end if
+
+            #if str($region.value) != '':
+                --region '$region'
+            #end if
+]]>
+    </command>
+
+    <inputs>
+        <expand macro="multiple_input_bigwigs" />
+
+        <conditional name="mode">
+            <param name="modeOpt" type="select" label="Choose computation mode"
+                help="In the bins mode, the correlation is computed using equally sized bins.
+                In the BED file mode, a list of genomic regions in BED format has to be given.
+                For each region in the BED file, the number of overlapping reads is counted in
+                each of the BigWig files. Then the correlation is computed.">
+                <option value="bins" selected="true">Bins</option>
+                <option value="BED-file">Limit correlation to certain regions (BED file)</option>
+            </param>
+            <when value="bins">
+                <param name="binSize" type="integer" value="10000" min="1"
+                    label="Bin size in bp"
+                    help="Length in bases for a window used to sample the genome. (--binSize)"/>
+
+                <expand macro="distanceBetweenBins" />
+            </when>
+            <when value="BED-file">
+                <param name="region_file" type="data" format="bed"
+                    label="Region file in BED format"
+                    help="Correlation is computed for the number of reads that overlap such regions."/>
+            </when>
+        </conditional>
+
+        <expand macro="region_limit_operation" />
+        <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/>
+
+    </inputs>
+    <outputs>
+        <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" />
+        <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
+            <filter>outRawCounts is True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
+            <param name="modeOpt" value="bins" />
+            <param name="binSize" value="10" />
+            <param name="corMethod" value="spearman" />
+            <output name="outFileName" file="multiBigwigSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
+        </test>
+        <!--test>
+            <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
+            <param name="modeOpt" value="BED-file" />
+            <param name="region_file" value="multiBamSummary_regions.bed" />
+            <param name="corMethod" value="pearson" />
+            <param name="outRawCounts" value="True" />
+            <output name="outFileRawCounts" file="multiBigwigSummary_result2.tabular" ftype="tabular" />
+            <output name="outFileName" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
+        </test-->
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Given two or more bigWig files, multiBigwigSummary computes the average scores for each of the files in every genomic region.
+This analysis is performed for the entire genome by running the program in 'bins' mode, or for certain user selected regions
+in 'BED-file' mode. Typically the output of multiBigwigSummary is used by other tools, such as 'plotCorrelation' or 'plotPCA',
+for visualization and diagnostic purposes.
+
+
+**Output files**:
+
+- **Coverage scores**: Coverage scores computed and saved in a format appropriate for 'plotCorrelation' or 'plotPCA'.
+
+- Data matrix (optional,select to save raw counts to a file above): If you want to have a look at the coverage values
+  or compute statistics yourself using a different program (like R).
+
+-----
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>