--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/find_qPCR_regions.xml	Sat Apr 28 15:07:26 2018 -0400
@@ -0,0 +1,35 @@
+<tool id="find_qPCR_regions" name="Find ATAC qPCR regions" version="0.1.0">
+    <description> Determines optimal regions for designing ATAC-qPCR primers.</description>
+    <requirements>
+        <requirement type="package" version="3.4.2" >r-base</requirement>
+    </requirements>
+    <command><![CDATA[
+        Rscript --vanilla $__tool_directory__/find_qPCR_regions.R $input1 $input2 $input3 $input4 $input5 $output
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="tabular" label="Coverage Bed File"/>
+        <param type="data" name="input2" format="tabular" label="Spanning Fragment Coverage Bed File"/>
+        <param type="data" name="input3" format="tabular" label="Total Read Counts"/>
+        <param type="float" name="input4" value="0.8" label="Correlation Cutoff"/>
+        <param type="integer" name="input5" value="3" label="Coverage Cutoff"/>
+    </inputs>
+    <outputs>
+	<data name="output" format="bed" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="combined.o.bed.coverage"/>
+            <param name="input2" value="combined.f9.bed.coverage"/>
+            <param name="input3" value="lib_sizes.txt"/>
+            <param name="input4" value="0.7"/>
+            <param name="input5" value="2"/>
+            <output name="output" file="qPCR_regions.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Determines optimal regions for designing ATAC-qPCR primers based on correlation between spanning fragments and total peak height. 
+    ]]></help>
+    <citations>
+        <citation type="doi">doi:10.1038/nmeth.4663</citation>
+    </citations>
+</tool>