--- a/hyphy_gard.xml	Tue Dec 04 11:12:01 2018 -0500
+++ b/hyphy_gard.xml	Mon Feb 18 15:12:22 2019 -0500
@@ -5,44 +5,24 @@
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="1.0.4">
-    translate-gard</requirement>
+    <requirement type="package" version="1.0.4">translate-gard</requirement>
   </expand>
-  <version_command>HYPHYMP --version | tail -n 1 | awk '{print
-  $1}'</version_command>
+  <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
   <command detect_errors="exit_code"><![CDATA[
-    export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} &&
+    export MPI_NODE_COUNT=\${GALAXY_SLOTS:-2} &&
     ln -s '$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 $rate_cond.rate_classes >> tool_params &&
     #end if
-    echo `pwd`/"gard_input.fa.GARD.json" >> tool_params &&
+    echo `pwd`/"gard_input.GARD" >> tool_params &&
     @HYPHYMPI_INVOCATION@ \$HYPHYMPI_LIB/TemplateBatchFiles/GARD.bf > '$gard_log' &&
-    translate-gard -i gard_input.fa -j gard_input.fa.GARD.json -o gard_input.fa.translated.json
+    translate-gard -i gard_input.GARD -j gard_input.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>
@@ -60,14 +40,13 @@
   </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"/>
+    <data name="gard_output" format="nex" from_work_dir="gard_input.GARD_finalout"/>
+    <data name="translated" format="hyphy_json_results" 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"/>
+      <param name="input_file" ftype="fasta" value="gard-in1.fa"/>
+      <output name="gard_output" file="gard-out1.nex" compare="sim_size" delta="160000"/>
     </test>
   </tests>
   <help><![CDATA[