--- a/macros.xml	Wed Aug 24 17:58:18 2022 +0000
+++ b/macros.xml	Tue Feb 03 18:50:29 2026 +0000
@@ -1,13 +1,14 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">4.1.7.0</token>
-    <token name="@WRAPPER_VERSION@">@VERSION@+galaxy1</token>
+    <token name="@TOOL_VERSION@">4.6.2.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">24.1</token>
 
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">gatk4</requirement>
-            <requirement type="package" version="0.2.5">tabix</requirement>
-            <requirement type="package" version="1.9">samtools</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">gatk4</requirement>
+            <requirement type="package" version="1.11">tabix</requirement>
+            <requirement type="package" version="1.23">samtools</requirement>
             <yield />
         </requirements>
     </xml>
@@ -654,6 +655,52 @@
         <!--#end if-->
     <!--</template>-->
 
+    <token name="@GATK_LINK_REF@"><![CDATA[
+    ## 1. Link Reference Genome
+    #if $reference_source.reference_source_selector == "history":
+        ln -s '$reference_source.reference_sequence' reference.fa &&
+        samtools faidx reference.fa &&
+    #else:
+        ln -s '$reference_source.reference_sequence.fields.path' reference.fa &&
+        ln -s '${reference_source.reference_sequence.fields.path}.fai' reference.fa.fai &&
+    #end if
+    
+    ## Ensure dictionary exists
+    gatk CreateSequenceDictionary -R reference.fa &&
+    ]]></token>
+
+    <xml name="gatk_ref_source">
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+                <option value="cached">Locally cached</option>
+                <option value="history" selected="true">History</option>
+            </param>
+            <when value="cached">
+                <param name="reference_sequence" type="select" label="Reference" help="Select reference genome">
+                    <options from_data_table="all_fasta" />
+                </param>
+            </when>
+            <when value="history">
+                <param name="reference_sequence" type="data" format="fasta" label="Reference" help="Select reference genome from history" />
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="gatk_param_intervals">
+        <param name="intervals" argument="-L" type="data" format="picard_interval_list" optional="true" label="Interval List" help="One or more genomic intervals over which to operate." />
+    </xml>
+
+    <xml name="gatk_param_known_sites">
+        <param argument="--known-sites" type="data" format="vcf_bgzip" multiple="true" label="Known Sites" help="VCF file(s) (e.g., dbSNP, Mills) masking known sites." />
+    </xml>
+
+    <xml name="gatk_param_use_original_qualities">
+        <param argument="--use-original-qualities" type="boolean" truevalue="--use-original-qualities" falsevalue="" checked="true" label="Use Original Qualities" help="Use the OQ tag if present." />
+    </xml>
+
+    <xml name="gatk_param_add_output_sam_program_record">
+        <param argument="--add-output-sam-program-record" type="boolean" truevalue="--add-output-sam-program-record" falsevalue="" checked="true" label="Add Output SAM Program Record" help="Adds an extra PG tag to the header." />
+    </xml>
 
     <!--Citations-->
     <xml name="citations">