--- a/macros.xml	Wed Jul 26 20:02:13 2023 +0000
+++ b/macros.xml	Wed Mar 19 17:25:56 2025 +0000
@@ -3,6 +3,7 @@
 
     <token name="@TOOL_VERSION@">2.2.1</token>
     <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE_VERSION@">20.01</token>
 
     <xml name="xrefs">
         <xrefs>
@@ -29,10 +30,14 @@
 
     <token name="@set_reference_fasta_filename@"><![CDATA[
     #if str( $reference_source.reference_source_selector ) == "history":
-        #set $reference_fasta_filename = "localref.fa"
-        ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
-        bwa-mem2 index
-        '${reference_fasta_filename}' &&
+        #if $reference_source.ref_file.is_of_type("bwa_mem2_index"):
+            #set $reference_fasta_filename = $reference_source.ref_file.extra_files_path + "/reference"
+        #else
+            #set $reference_fasta_filename = "localref." + $reference_source.ref_file.extension
+            ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
+            bwa-mem2 index
+            '${reference_fasta_filename}' &&
+        #end if
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
@@ -41,7 +46,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bwa-mem2</requirement>
-            <requirement type="package" version="1.13">samtools</requirement>
+            <yield></yield>
         </requirements>
     </xml>
 
@@ -59,7 +64,7 @@
         <conditional name="reference_source">
             <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
                 <option value="cached">Use a built-in genome index</option>
-                <option value="history">Use a genome from history and build index</option>
+                <option value="history">Use a reference from history and build index if necessary</option>
             </param>
             <when value="cached">
                 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
@@ -71,7 +76,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
+                <param name="ref_file" type="data" format="fasta,fasta.gz,bwa_mem2_index" label="Use the following dataset as the reference" help="You can upload a FASTA sequence to the history and use it as reference. For better performance build a reference index separately." />
             </when>
         </conditional>
     </macro>