From bf7797924202b1f0d47ebdc53e725e6b6d3273b6 Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Mon, 4 Nov 2024 04:26:33 +0000
Subject: [PATCH 1/4] Updating tools/freyja from version 1.5.1 to 1.5.2

---
 tools/freyja/macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/freyja/macros.xml b/tools/freyja/macros.xml
index b797ae5403e..7f392aa55d4 100644
--- a/tools/freyja/macros.xml
+++ b/tools/freyja/macros.xml
@@ -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">

From 4ac519d568b1f02bdf5058f6c751c0a175afbd2c Mon Sep 17 00:00:00 2001
From: Saim Momin <mominsaim12@gmail.com>
Date: Fri, 15 Nov 2024 15:57:12 +0100
Subject: [PATCH 2/4] Update freyja to 1.5.2 and add --pathogen option

---
 tools/freyja/macros.xml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/tools/freyja/macros.xml b/tools/freyja/macros.xml
index 7f392aa55d4..25183633fd5 100644
--- a/tools/freyja/macros.xml
+++ b/tools/freyja/macros.xml
@@ -39,6 +39,7 @@ ln -s '$variants_file' 'variants_file.vcf' &&
     --meta '${meta}'
 #end if
 $confirmedonly
+$pathogen
 ]]></token>
     <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
 #if $usher_update_option.choice == 'custom'
@@ -138,6 +139,17 @@ freyja plot
                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=""

From 14601b6e00a7195313bec02a4d502e77d322590b Mon Sep 17 00:00:00 2001
From: Saim Momin <mominsaim12@gmail.com>
Date: Fri, 15 Nov 2024 16:17:14 +0100
Subject: [PATCH 3/4] Minor change to macros

---
 tools/freyja/macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/freyja/macros.xml b/tools/freyja/macros.xml
index 25183633fd5..27fdd996c15 100644
--- a/tools/freyja/macros.xml
+++ b/tools/freyja/macros.xml
@@ -39,7 +39,7 @@ ln -s '$variants_file' 'variants_file.vcf' &&
     --meta '${meta}'
 #end if
 $confirmedonly
-$pathogen
+--pathogen $pathogen
 ]]></token>
     <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
 #if $usher_update_option.choice == 'custom'

From d4a17f8dbec06bdce69689b489447a839a666108 Mon Sep 17 00:00:00 2001
From: Saim Momin <mominsaim12@gmail.com>
Date: Fri, 15 Nov 2024 16:33:18 +0100
Subject: [PATCH 4/4] Minor change

---
 tools/freyja/macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/freyja/macros.xml b/tools/freyja/macros.xml
index 27fdd996c15..994d7dc3fa3 100644
--- a/tools/freyja/macros.xml
+++ b/tools/freyja/macros.xml
@@ -39,7 +39,7 @@ ln -s '$variants_file' 'variants_file.vcf' &&
     --meta '${meta}'
 #end if
 $confirmedonly
---pathogen $pathogen
+--pathogen '$pathogen'
 ]]></token>
     <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
 #if $usher_update_option.choice == 'custom'