# HG changeset patch
# User iuc
# Date 1739963324 0
# Node ID 11c062caec10dab2a2dabace1eed36d5eaf2a06a
# Parent  d17f930148a53640a6dabc794461bed427e00bbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06

diff -r d17f930148a5 -r 11c062caec10 macros.xml
--- a/macros.xml	Fri Nov 15 16:44:19 2024 +0000
+++ b/macros.xml	Wed Feb 19 11:08:44 2025 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.5.2</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
         <xrefs>
@@ -22,6 +22,16 @@
     freyja update &&
 #end if
 ]]></token>
+    <token name="@CUSTOM_BARCODES_LINKING@"><![CDATA[
+#if $usher_update_option.choice == 'custom'
+    ln -s '${usher_update_option.usher_barcodes}' usher_barcodes.csv &&
+#end if
+    ]]></token>
+    <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
+#if $usher_update_option.choice == 'custom'
+    --barcodes usher_barcodes.csv
+#end if
+]]></token>
     <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[
 ln -s '$variants_file' 'variants_file.vcf' &&
 ]]></token>
@@ -41,11 +51,6 @@
 $confirmedonly
 --pathogen '$pathogen'
 ]]></token>
-    <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
-#if $usher_update_option.choice == 'custom'
-    --barcodes '${usher_update_option.usher_barcodes}'
-#end if
-]]></token>
     <token name="@DASH_COMMAND@"><![CDATA[
 echo '${plot_format.plot_title}' > plot_title.txt &&
 echo '${plot_format.plot_intro}' > plot_intro.txt &&