--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/window_coverage.xml	Sat Apr 28 15:07:26 2018 -0400
@@ -0,0 +1,38 @@
+<tool id="window_coverage" name="Calculate window coverage" version="0.1.0">
+    <description> Determines spanning and total read coverage for overlapping windows spanning peaks of interest. </description>
+    <requirements>
+        <requirement type="package" version="1.3">samtools</requirement>
+        <requirement type="package" version="2.27.0.0">bedtools</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        #set input_list = '","'.join( [str( $input.name ) for $input in $input1 ] )
+        $__tool_directory__/./window_coverage.bash "$input1" "$input_list" "$input2" "$input3" "$output1" "$output2"
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="bam" multiple="true" label="Filtered Bam Files"/>
+        <param type="data" name="input2" format="bed" label="qPCR Window Bed File"/>
+        <param type="float" name="input3" value="0.9" label="Coverage Cutoff"/>
+    </inputs>
+    <outputs>
+        <data name="output1" format="bed" label="Coverage Bed File"/>
+        <data name="output2" format="bed" label="Spanning Fragment Coverage Bed File" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="Ch1-1.pe.q10.sort.bam.rmdup.filter.bam,Ch13-1.pe.q10.sort.rmdup.filter.bam"/>
+            <param name="input2" value="qPCR_windows.bed" />
+            <param name="input3" value="0.9" />
+            <output name="output1" file="combined.o.coverage"/>
+            <output name="output2" file="combined.f9.coverage"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tools takes a series of bam files and a bed file of overlapping windows spanning peaks of interest and determines the read coverage and spanning fragment coverage for each window.  
+    ]]></help>
+    <citations>
+        <citation type="doi">doi:10.1038/nmeth.4663</citation>
+    </citations>
+</tool>