--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_window_bed.xml	Sat Apr 28 15:07:26 2018 -0400
@@ -0,0 +1,29 @@
+<tool id="make_window_bed" name="Create bed file of qPCR windows" version="0.1.0">
+    <description> Creates bed file of windows spanning peaks of interest.</description>
+        <requirements>
+            <requirement type="package" version="3.4.2">r-base</requirement>
+    </requirements>
+    <command><![CDATA[
+        Rscript --vanilla $__tool_directory__/make_window_bed.R $input1 $input2 $output
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="bed" label="Peak Bed File"/>
+        <param type="integer" name="input2" value="100" label="Window Size"/>
+    </inputs>
+    <outputs>
+	<data name="output" format="bed" label="qPCR Window Bed File"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="RAMA_peaks.bed"/>
+            <param name="input2" value="100"/>
+            <output name="output" file="qPCR_windows.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Generates bed file containing overlapping windows of specified size spanning peaks in input bed file. 
+    ]]></help>
+    <citations>
+        <citation type="doi">doi:10.1038/nmeth.4663</citation>
+    </citations>
+</tool>