--- a/macros.xml	Thu Aug 18 13:51:18 2022 +0000
+++ b/macros.xml	Thu Mar 02 15:17:27 2023 +0000
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">2.5.36</token>
+    <token name="@TOOL_VERSION@">2.5.47</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.05</token>
+
     <xml name="inputs">
 	    <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" />
         <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>
@@ -10,8 +13,8 @@
             <xref type="bio.tools">HyPhy</xref>
         </xrefs>
     </xml>
-    <xml name="substitution">
-        <param name="model" type="select" label="Substitution model">
+    <xml name="substitution" tokens="argument">
+        <param argument="@ARGUMENT@" type="select" label="Substitution model">
             <option value="GTR">GTR - General time reversible
             model</option>
             <option value="LG">LG - Generalist empirical model from
@@ -66,13 +69,13 @@
 
     <xml name="mcmc_options">
         <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" />
-        <param argument="--chain-length" name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" />
+        <param argument="--chain-length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" />
         <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" />
         <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" />
     </xml>
 
     <xml name="gencode">
-        <param name="gencodeid" type="select" label="Genetic code">
+        <param argument="--code" name="gencodeid" type="select" label="Genetic code">
             <option value="Universal">Universal code</option>
             <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA
             code</option>
@@ -119,7 +122,7 @@
 
     <xml name="branches">
         <conditional name="branch_cond">
-            <param name="branch_sel" type="select" label="Set of branches to test">
+            <param argument="--branches" name="branch_sel" type="select" label="Set of branches to test">
                 <option value="All">All branches</option>
                 <option value="Internal">Internal branches</option>
                 <option value="Leaves">Leaf branches</option>
@@ -152,7 +155,7 @@
         </requirements>
     </xml>
     <xml name="alternative_model_output">
-        <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json">
+        <data name="alternative_model" format="nhx" from_work_dir="alternative_model.nhx" label="${tool.name} on ${on_string}: Alternative model">
             <filter>advanced['save_alternative_model']</filter>
         </data>
     </xml>
@@ -188,7 +191,7 @@
             --rates $advanced.rates
             --srv $advanced.srv
             #if $advanced.save_alternative_model:
-                --save-fit alternative_model.json
+                --save-fit alternative_model.nhx
             #end if
         #end if
     ]]></token>