--- a/hyphy_relax.xml	Tue Apr 20 19:55:48 2021 +0000
+++ b/hyphy_relax.xml	Tue Apr 27 18:03:51 2021 +0000
@@ -1,11 +1,9 @@
 <?xml version="1.0"?>
-<tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0" profile="19.09">
+<tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy1" profile="19.09">
     <description>Detect relaxed selection in a codon-based
     phylogenetic framework</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@OPERATION@">RELAX</token>
-        <token name="@operation@">relax</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
@@ -13,42 +11,56 @@
         export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" &&
         hyphy relax
             --alignment ./$input_file
-            #if $input_nhx:
-                --tree ./input.nhx
-            #end if
-            --models '$analysisType'
+            @INPUT_TREE@
+            --models '$models'
             --code '$gencodeid'
-            #if $treeAnnotations == "2":
-                --test TEST
-                --reference REFERENCE
-            #else:
-                --test TEST
+            --test '$test'
+            #if $reference:
+                --reference '$reference'
             #end if
-            > '$relax_log' ;
-        @CATCH_ERROR@
+            @advanced_options@
+            --output '$relax_output'
+        @ERRORS@
     ]]></command>
     <inputs>
         <expand macro="inputs"/>
         <expand macro="gencode"/>
-        <param argument="--model" name="analysisType" type="select" label="Analysis Type" >
+        <param argument="--models" type="select" label="Analysis Type" >
             <option value="All">All</option>
             <option value="Minimal">Minimal</option>
         </param>
-        <param name="treeAnnotations" type="select" label="Tree Annotations" help = "Is there one or two sets of annotated branches in the Newick file?">
-            <option value="1">TEST only</option>
-            <option value="2">TEST and REFERENCE</option>
+        <param argument="--test" type="text" value="Unlabeled branches" optional="false" label="Branches to use as the test set">
+            <sanitizer invalid_char="">
+                <valid initial="default" />
+            </sanitizer>
         </param>
+        <param argument="--reference" type="text" optional="true" label="Branches to use as the reference set">
+            <sanitizer invalid_char="">
+                <valid initial="default" />
+            </sanitizer>
+        </param>
+        <expand macro="srv" />
     </inputs>
     <outputs>
-        <data name="relax_log" format="txt"/>
         <data name="relax_output" format="hyphy_results.json"/>
+        <expand macro="alternative_model_output" />
     </outputs>
     <tests>
         <test>
             <param name="input_file" ftype="fasta" value="relax-in1.fa"/>
             <param name="input_nhx" ftype="nhx" value="relax-in1.nhx"/>
+            <param name="test" value="TEST" />
             <output name="relax_output" file="relax-out1.json" compare="sim_size"/>
         </test>
+        <test>
+            <param name="input_file" ftype="nex" value="relax-in2.nex"/>
+            <param name="srv_options" value="specify" />
+            <param name="save_alternative_model" value="true" />
+            <param name="test" value="PR" />
+            <param name="srv" value="Yes" />
+            <output name="relax_output" file="relax-out2-1.json" compare="sim_size"/>
+            <output name="alternative_model" file="relax-out2-2.json" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
 RELAX: a test for selection differences