--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/multiBamSummary.xml	Mon Jan 25 20:18:00 2016 -0500
@@ -0,0 +1,132 @@
+<tool id="deeptools_multi_bam_summary" name="multiBamSummary" version="@WRAPPER_VERSION@.0">
+    <description>calculates average read coverages for a list of two or more BAM files</description>
+    <macros>
+        <token name="@BINARY@">multiBamSummary</token>
+        <import>deepTools_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+<![CDATA[
+        #set files=[]
+        #set labels=[]
+
+        @multiple_input_bams@
+        @BINARY@
+            $mode.modeOpt
+            @THREADS@
+
+            --outFileName '$outFile'
+            --bamfiles '#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).strip() != '':
+                --region '$region'
+            #end if
+
+            #if $advancedOpt.showAdvancedOpt == "yes":
+                @ADVANCED_OPTS_READ_PROCESSING@
+            #end if
+]]>
+    </command>
+
+    <inputs>
+        <expand macro="multiple_input_bams" />
+
+        <conditional name="mode">
+            <param name="modeOpt" type="select" label="Choose computation mode" 
+                    help="In the bins mode, the coverage is computed for equally
+                    sized bins. In the BED file mode, a list of genomic regions in BED
+                    format has to be given. For each region in the BED file the number of
+                    overlapping reads is counted in each of the BAM files.
+                    ">
+                <option value="bins" selected="true">Bins</option>
+                <option value="BED-file">Limit calculation to certain regions (BED file)</option>
+            </param>
+            <when value="bins">
+                <param name="binSize" type="integer" value="10000" min="1"
+                    label="Bin size in bp"
+                    help="Length in bases of the window used to sample the genome. (--binSize)"/>
+
+                <expand macro="distanceBetweenBins" />
+
+            </when>
+            <when value="BED-file">
+                <param name="region_file" type="data" format="bed"
+                    label="Region file in BED format"
+                    help="Coverage is computed for the number of reads that overlap such regions."/>
+            </when>
+        </conditional>
+
+        <expand macro="region_limit_operation" />
+
+        <expand macro="advancedOpt_scaffold">
+            <expand macro="read_processing_options" />
+        </expand>
+
+        <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/>
+
+    </inputs>
+    <outputs>
+        <data format="deeptools_coverage_matrix" name="outFile" label="${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="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
+            <param name="modeOpt" value="bins" />
+            <param name="binSize" value="10" />
+            <output name="outFile" file="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
+        </test>
+        <test>
+            <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
+            <param name="modeOpt" value="BED-file" />
+            <param name="region_file" value="multiBamSummary_regions.bed" />
+            <output name="outFile" file="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
+        </test>
+
+
+    </tests>
+    <help>
+<![CDATA[
+
+**What it does**
+
+This tool generates a matrix of read-coverages for a list of genomic regions and at least two samples (BAM files).
+The genome is split into bins of the given size. For each bin, the number of reads found in it in each BAM file is counted.
+Alternatively, a bed file with pre-defined genomic regions can be provided. In each case the calculation can further be limited to
+a given genomic interval (e.g. a given chromosome). This option is mostly used for testing and efficiency.
+A typical follow-up application is to check and visualize the similarity between replicates or published data sets (see: plotPCA and plotCorrelation).
+
+**Output files**:
+
+- **score matrix**: a compressed matrix where every row corresponds to a genomic region (or bin) and each column corresponds to a sample (BAM file)
+- Optional : Uncompressed **score matrix**, in case you want to analyse the coverage scores yourself. (Select to "Save raw counts" from above)
+
+=======
+
+.. image:: $PATH_TO_IMAGES/QC_multiBamSummary_humanSamples.png
+   :alt: Heatmap of RNA Polymerase II ChIP-seq
+
+
+You can find more details on the multiBamSummary doc page: https://deeptools.readthedocs.org/en/master/content/tools/multiBamSummary.html
+
+-----
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>