--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sarscov2summary.xml	Mon May 04 05:42:35 2020 -0400
@@ -0,0 +1,61 @@
+<tool id="sarscov2summary" name="sarscov2summary" version="0.1" profile="18.01">
+    <requirements>
+        <requirement type="package" version="0.5">sarscov2summary</requirement>
+    </requirements>
+    <command><![CDATA[
+sarscov2summary
+-s '$slac'
+-f '$fel'
+-m '$meme'
+-p '$prime'
+-P $pvalue
+-c '$coords'
+-D '$db'
+-d '$dups'
+    ]]></command>
+    <inputs>
+        <param name ="slac" type="data" format="json" label="HyPhy SLAC Output" />
+        <param name ="fel" type="data" format="json" label="HyPhy FEL Output" />
+        <param name ="meme" type="data" format="json" label="HyPhy MEME Output" />
+        <param name ="prime" type="data" format="json" label="HyPhy PRIME Output" />
+        <param name="pvalue" type="float" value="0.1" label="P-value" />
+        <param name="coords" type="data" format="fasta" label="Alignment With Reference" />
+        <param name="db" type="data" format="json" label="Metadata" />
+        <param name="dups" type="data" format="json" label="Duplicates" />
+    </inputs>
+    <outputs>
+        <data name="summary" format="json" from_work_dir="summary.json" label="Summary" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="slac" ftype="json" value="slac.json" />
+            <param name="fel" ftype="json" value="fel.json" />
+            <param name="meme" ftype="json" value="meme.json" />
+            <param name="prime" ftype="json" value="prime.json" />
+            <param name="coords" ftype="fasta" value="align.fasta" />
+            <param name="db" ftype="json" value="meta.json" />
+            <param name="dups" ftype="json" value="dups.json" />
+            <output name="summary" ftype="json" compare="diff" value="summary.json" />
+        </test>
+    </tests>
+        <help><![CDATA[
+===============
+sarscov2summary
+===============
+
+Custom summary script for the SARS-CoV2 Selection Analysis workflow. Takes HyPhy outputs as well as metadata to create final summary output.
+
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @misc{githubsarscov2summary,
+            author = {Sergei Pond},
+            year = {2020},
+            title = {sarscov2summary},
+            publisher = {Github},
+            journal = {Github repository},
+            url = {https://github.com/nickeener/sarscov2summary},
+        }</citation>
+    </citations>
+</tool>