--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dnds.xml	Mon Dec 04 10:25:26 2017 -0500
@@ -0,0 +1,41 @@
+<tool id="dnds" name="dNdS Report" version="0.1.0">
+    <description>Calculate the dN/dS value for each region in a bed file</description>
+    <requirements>
+          <requirement type="package" version="0.2.2">quasitools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+
+        quasitools dnds $csv_file $ref_file $offset -o output.csv
+
+    ]]></command>
+    <inputs>
+        <param name="csv_file" type="data" format="csv" optional="false" label="CSV file" />
+        <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
+        <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/>
+    </inputs>
+    <outputs>
+        <data format="csv" name="output" from_work_dir="output.csv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="csv_file" value="mutant_types.csv" />
+            <param name="ref_file" value="hxb2_pol.fas" />
+            <output name="output" ftype="csv" >
+                <assert_contents>
+                    <has_text_matching expression="#gene,pn,ps,pn_sites,ps_sites,dn/ds"/>
+                    <has_text text="RT,0.0334,0.0111,1,1,3.0539" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+dNdS Report
+===================
+
+Determines the dNdS ratio for each codon variant in a supplied csv file (codon variants).
+
+    ]]></help>
+    <citations>
+    </citations>
+</tool>
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