--- a/macros.xml	Tue Jul 13 14:01:12 2021 +0000
+++ b/macros.xml	Sat Sep 25 18:21:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">0.4.1</token>
+    <token name="@TOOL_VERSION@">0.4.3</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">20.05</token>
     <xml name="requirements">
         <requirements>
@@ -14,7 +15,7 @@
                 <option value="history">Use a FASTA from history</option>
             </param>
             <when value="cached">
-                <param name="ref_file" type="select" label="Use built-in FASTA" help="Select genome from the list">
+                <param name="ref_file" argument="--reference" type="select" label="Use built-in FASTA" help="Select genome from the list">
                     <options from_data_table="all_fasta">
                         <filter type="sort_by" column="2" />
                         <validator type="no_options" message="No reference genomes are available" />
@@ -23,10 +24,10 @@
                 </param>
             </when>
             <when value="history">
-                <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the FASTA" help="You can upload a FASTA sequence to the history and use it as reference" />
+                <param name="ref_file" argument="--reference" type="data" format="fasta" label="Use the following dataset as the FASTA" help="You can upload a FASTA sequence to the history and use it as reference" />
             </when>
         </conditional>
-        <param name="Reference" type="data" format="bed" label="Reference 3'UTRs BED file" />
+        <param argument="--reference" type="data" format="bed" label="Reference 3'UTRs BED file" />
     </xml>
     <xml name="citations">
         <citation type="doi">