From 0821b18dd8d6bf06fd1ca3966bad1aabfddf39ac Mon Sep 17 00:00:00 2001
From: tlacroix <thomas.lacroix@inra.fr>
Date: Tue, 14 Apr 2026 11:00:35 +0200
Subject: [PATCH] update ppanggolin suite: changed output file
 partition_genome_alignment format to fasta in order to improve
 interoperability with other tools (i.e. fasttree)

---
 tools/ppanggolin/macros.xml         | 2 +-
 tools/ppanggolin/ppanggolin_msa.xml | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/ppanggolin/macros.xml b/tools/ppanggolin/macros.xml
index 91354662bf3..c924400ce14 100644
--- a/tools/ppanggolin/macros.xml
+++ b/tools/ppanggolin/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.3.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="citation">
         <citations>
             <citation type="doi">10.1371/journal.pcbi.1007732</citation> 
diff --git a/tools/ppanggolin/ppanggolin_msa.xml b/tools/ppanggolin/ppanggolin_msa.xml
index f6f5908b196..9866020c899 100644
--- a/tools/ppanggolin/ppanggolin_msa.xml
+++ b/tools/ppanggolin/ppanggolin_msa.xml
@@ -74,7 +74,7 @@
             <option value="dna">DNA</option>
         </param>
         
-        <param argument="--phylo" name="do_phylo" type="boolean" checked="true" label="Writes a whole genome msa file for additional phylogenetic analysis (recommended)" truevalue="--phylo" falsevalue=""/>
+        <param argument="--phylo" name="do_phylo" type="boolean" checked="true" label="Writes a whole genome msa file (fasta format) for additional phylogenetic analysis (recommended)" truevalue="--phylo" falsevalue=""/>
 
         <param argument="--single_copy" name="do_single_copy" type="boolean" checked="false" label="Report gene families that are considered 'single copy'" truevalue="--single_copy" falsevalue=""/>
 
@@ -84,7 +84,7 @@
 
     <outputs>
         <data name="archive_msa_partition_source" format="tar.gz" label="PPanGGOLiN msa on ${on_string}: archive msa ${choice_partition} ${choice_source}" />
-        <data name="partition_genome_alignment" format="maf" label="PPanGGOLiN msa on ${on_string}: ${choice_partition} genome alignment" >
+        <data name="partition_genome_alignment" format="fasta" label="PPanGGOLiN msa on ${on_string}: ${choice_partition} genome alignment" >
           <filter>do_phylo is True</filter>
         </data>
     </outputs>