--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/paired_end_cross_plot.xml	Thu Mar 10 10:34:37 2016 -0500
@@ -0,0 +1,58 @@
+<tool id="paired_end_cross_plot" name="Paired-end cross plot" version="1.0.0">
+    <description></description>
+    <command>
+        <![CDATA[
+            java -jar $__tool_directory__/pairedendCrossPlot.jar
+            -f "$input1"
+            -r "$input2"
+            -w $window_size
+            -o "$output" 1>/dev/null
+        ]]>
+    </command>
+    <inputs>
+        <param name="input1" type="data" format="scidx" label="Read 1 ScIdx file" />
+        <param name="input2" type="data" format="scidx" label="Read 2 ScIdx file" />
+        <param name="window_size" type="integer" value="500" min="1" label="Size of window upstream and downstream around the reference point in base pairs" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="input1.scidx" ftype="scidx"/>
+            <param name="input2" value="input2.scidx" ftype="scidx"/>
+            <param name="window_size" value="500"/>
+            <output name="output" file="output1.tabular" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input1" value="input3.scidx" ftype="scidx"/>
+            <param name="input2" value="input4.scidx" ftype="scidx"/>
+            <param name="window_size" value="500"/>
+            <output name="output" file="output2.tabular" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Produces a frequency histogram of the relative occurrence of Read2 5' ends relative to the
+start of every Read1 5' end in a user-specified coordinate window.
+
+-----
+
+**Options**
+
+* **Window Size** - sets the size of the window upstream and downstream around the reference point in base pairs.
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{None,
+            author = {Lai, William},
+            title = {None},
+            year = {None},
+            eprint = {None},
+            url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
+        }</citation>
+    </citations>
+</tool>