# HG changeset patch
# User iuc
# Date 1731689082 0
# Node ID 54acd5139cab8a6833db35f4a6924b327afe1932
# Parent  948903a8555dc45a802c7de8f38aa3ae0c080206
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859

diff -r 948903a8555d -r 54acd5139cab macros.xml
--- a/macros.xml	Thu Oct 10 18:28:32 2024 +0000
+++ b/macros.xml	Fri Nov 15 16:44:42 2024 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.5.1</token>
+    <token name="@TOOL_VERSION@">1.5.2</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
@@ -39,6 +39,7 @@
     --meta '${meta}'
 #end if
 $confirmedonly
+--pathogen '$pathogen'
 ]]></token>
     <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
 #if $usher_update_option.choice == 'custom'
@@ -138,6 +139,17 @@
                checked="false"
                label="Use larger library with non-public lineages"
                help="Allows to use larger UShER barcodes library extended with GISAID non-public lineages"/>
+        <param argument="--pathogen" type="select" label="Pathogen of interest">
+            <option value="SARS-CoV-2" selected="true">SARS-CoV-2</option>
+            <option value="MPXV" selected="true">MPXV</option>
+            <option value="H5NX" selected="true">H5NX</option>
+            <option value="H1N1pdm" selected="true">H1N1pdm</option>
+            <option value="FLU-B-VIC" selected="true">FLU-B-VIC</option>
+            <option value="MEASLESN450" selected="true">MEASLESN450</option>
+            <option value="MEASLES" selected="true">MEASLES</option>
+            <option value="RSVa" selected="true">RSVa</option>
+            <option value="RSVb" selected="true">RSVb</option>
+        </param> 
     </xml>
     <xml name="plot_lineages">
         <param argument="--lineages" type="boolean" truevalue="--lineages" falsevalue=""