--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hyphy_gard.xml	Tue Dec 04 10:45:05 2018 -0500
@@ -0,0 +1,79 @@
+<?xml version="1.0"?>
+<tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy0">
+  <description>: Recombination Detection</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements">
+    <requirement type="package" version="1.0.4">
+    translate-gard</requirement>
+  </expand>
+  <version_command>HYPHYMP --version | tail -n 1 | awk '{print
+  $1}'</version_command>
+  <command detect_errors="exit_code"><![CDATA[
+    export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} &&
+    ln -s '$input_file' gard_input.fa &&
+    echo `pwd`/gard_input.fa > tool_params &&
+    echo "010010" >> tool_params &&
+    echo $gencodeid >> tool_params &&
+    echo $rate_cond.rate >> tool_params &&
+    #if str($rate_cond.rate) != "1":
+        echo $rate_cond.rate_classes >> tool_params &&
+    #end if
+    echo `pwd`/"gard_input.fa.GARD.json" >> tool_params &&
+    @HYPHYMPI_INVOCATION@ \$HYPHYMPI_LIB/TemplateBatchFiles/GARD.bf > '$gard_log' &&
+    translate-gard -i gard_input.fa -j gard_input.fa.GARD.json -o gard_input.fa.translated.json
+    ]]></command>
+  <inputs>
+    <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
+    <param name="gencodeid" type="select" label="Genetic code">
+      <option value="1">Universal code</option>
+      <option value="2">Vertebrate mitochondrial DNA code</option>
+      <option value="3">Yeast mitochondrial DNA code</option>
+      <option value="4">Mold, Protozoan and Coelenterate mt;
+      Mycloplasma/Spiroplasma</option>
+      <option value="5">Invertebrate mitochondrial DNA
+      code</option>
+      <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear
+      code</option>
+      <option value="7">Echinoderm mitochondrial DNA code</option>
+      <option value="8">Euplotid Nuclear code</option>
+      <option value="9">Alternative Yeast Nuclear code</option>
+      <option value="10">Ascidian mitochondrial DNA code</option>
+      <option value="11">Flatworm mitochondrial DNA code</option>
+      <option value="12">Blepharisma Nuclear code</option>
+    </param>
+    <conditional name="rate_cond">
+      <param name="rate" type="select" label="Rate variation">
+        <option value="1">None</option>
+        <option value="2">General Discrete</option>
+        <option value="3">Beta-Gamma</option>
+      </param>
+      <when value="1"/>
+      <when value="2">
+        <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
+      </when>
+      <when value="3">
+        <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data name="gard_log" format="txt"/>
+    <data name="gard_output" format="json" from_work_dir="gard_input.fa.GARD.json"/>
+    <data name="translated" format="json" from_work_dir="gard_input.fa.translated.json"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_file" ftype="fasta" value="gard-in2.fa"/>
+      <output name="gard_output" file="gard-out1.json" compare="sim_size"/>
+      <output name="translated" file="gard-out2.json" compare="sim_size"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+GARD (Genetic Algorithm for Recombination Detection) is a method to screen a multiple sequence analysis for the presence of recombination and is extremely useful as a pre-processing step for selection inference. Because recombinant sequences cannot be adequately described with a single phylogenetic history, selection inference on recombinant data often leads to a significant increase in false positives. GARD alleviates this concern by comprehensively screening an alignment for recombination breakpoints and inferring a unique phylogenetic history for each detected recombination block.
+        ]]></help>
+  <expand macro="citations">
+    <citation type="doi">10.1093/molbev/msl051</citation>
+  </expand>
+</tool>