--- a/hyphy_absrel.xml	Tue Jan 08 10:54:39 2019 -0500
+++ b/hyphy_absrel.xml	Mon Feb 11 14:13:42 2019 -0500
@@ -1,11 +1,11 @@
 <?xml version="1.0"?>
 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0">
-    <description>: adaptive Branch Site REL</description>
+    <description>adaptive Branch Site Random Effects Likelihood</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
+    <expand macro="version_command" />
     <command detect_errors="exit_code">
     <![CDATA[
     ln -s '$input_file' absrel_input.fa &&
@@ -14,41 +14,29 @@
     echo `pwd`/absrel_input.fa >> tool_params &&
     echo `pwd`/absrel_input.nhx >> tool_params &&
     echo '$branches' >> tool_params &&
-    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf > '$absrel_log'
+    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
+    #if $log:
+        > '$absrel_log'
+    #end if
     ]]>
     </command>
     <inputs>
-        <param name="input_file" type="data" format="fasta" label="Input FASTA file" />
-        <param name="input_nhx" type="data" format="nhx" label="Input newick 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>
-        <param name="branches" type="select" label="Set of branches to test">
-            <option value="1">All branches</option>
-            <option value="2">Internal branches</option>
-            <option value="3">Leaf branches</option>
-            <option value="4">Unlabeled branches</option>
-        </param>
+        <expand macro="inputs" />
+        <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history" />
+        <expand macro="gencode" />
+        <expand macro="branches" />
     </inputs>
     <outputs>
-        <data name="absrel_log" format="txt" />
-        <data name="absrel_output" format="json" from_work_dir="absrel_input.fa.ABSREL.json" />
+        <data name="absrel_log" format="txt">
+            <filter>log</filter>
+        </data>
+        <data name="absrel_output" format="hyphy_json_results" from_work_dir="absrel_input.fa.ABSREL.json" />
     </outputs>
     <tests>
         <test>
             <param name="input_file" ftype="fasta" value="absrel-in1.fa" />
             <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" />
+            <param name="log" value="false" />
             <output name="absrel_output" file="absrel-out1.json" compare="sim_size" />
         </test>
     </tests>