# HG changeset patch
# User iuc
# Date 1739963316 0
# Node ID e7a2086a0f0392a710e66b254e399758b3c3a2e2
# Parent  c5f2ce99da6908d8163c3c7d194731f65aab5040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06

diff -r c5f2ce99da69 -r e7a2086a0f03 freyja_demix.xml
--- a/freyja_demix.xml	Fri Nov 15 16:44:54 2024 +0000
+++ b/freyja_demix.xml	Wed Feb 19 11:08:36 2025 +0000
@@ -18,6 +18,7 @@
 #else:
     #set $sn = str($sample_name.name)
 #end if
+@CUSTOM_BARCODES_LINKING@
 #set $in_file = $sn.replace(' ', '_') + '.' + $variants_in.ext
 ln -s '$variants_in' $in_file &&
 freyja demix
@@ -98,6 +99,24 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Test 03: Custom Usher Barcode sample -->
+        <test expect_num_outputs="1">
+            <param name="variants_in" value="variants.tsv"/>
+            <param name="depth_file" value="depths.tsv"/>
+            <conditional name="usher_update_option">
+                <param name="choice" value="custom"/>
+                <param name="usher_barcodes" location="https://zenodo.org/records/14888005/files/usher_barcodes.csv"/>
+            </conditional>
+            <conditional name="sample_name">
+                <param name="source" value="auto"/>
+            </conditional>
+            <output name="abundances">
+                <assert_contents>
+                    <has_n_columns n="2"/>
+                    <has_text text="AY.48"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 @HELP_HEADER@
diff -r c5f2ce99da69 -r e7a2086a0f03 macros.xml
--- a/macros.xml	Fri Nov 15 16:44:54 2024 +0000
+++ b/macros.xml	Wed Feb 19 11:08:36 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 &&