# HG changeset patch
# User iuc
# Date 1768915408 0
# Node ID b05be63162630b89035b67a8ba48e7ebc3f43f2f
# Parent  b6a78d286482bbf3c85d5c61f688ddc50467c0f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo commit 95eb601ee5e08ebcca551bd949b83e0b85718df8

diff -r b6a78d286482 -r b05be6316263 macros.xml
--- a/macros.xml	Fri Apr 11 11:23:50 2025 +0000
+++ b/macros.xml	Tue Jan 20 13:23:28 2026 +0000
@@ -1,5 +1,5 @@
 <macros>
-	<token name="@TOOL_VERSION@">1.5.2</token>
+	<token name="@TOOL_VERSION@">1.6.0</token>
 	<token name="@VERSION_SUFFIX@">0</token>
 	<token name="@PROFILE@">23.2</token>
 	<xml name="edam_ontology">
diff -r b6a78d286482 -r b05be6316263 panaroo.xml
--- a/panaroo.xml	Fri Apr 11 11:23:50 2025 +0000
+++ b/panaroo.xml	Tue Jan 20 13:23:28 2026 +0000
@@ -28,6 +28,7 @@
             --threshold '$advanced.matching_option.threshold'
             --family_threshold '$advanced.matching_option.family_threshold'
             --len_dif_percent '$advanced.matching_option.len_dif_percent'
+            --family_len_dif_percent '$advanced.matching_option.family_len_dif_percent'
             $advanced.matching_option.merge_paralogs
             --search_radius '$advanced.refind_option.search_radius'
             --refind_prop_match '$advanced.refind_option.refind_prop_match'
@@ -84,6 +85,7 @@
                         <param argument="--threshold" type="float" value="0.98" label="Sequence identity threshold" help="default: 0.98"/>
                         <param argument="--family_threshold" type="float" value="0.7" label="Protein family sequence identity threshold" help="default: 0.7"/>
                         <param argument="--len_dif_percent" type="float" value="0.98" label="Length difference cutoff" help="default: 0.98"/>
+                        <param argument="--family_len_dif_percent" type="float" value="0.0" label="Length difference cutoff at the gene family level" help="default: 0.0"/>
                         <param argument="--merge-paralogs" type="boolean" truevalue="--merge_paralogs" falsevalue="" label="Merge Paralogs"/>
                   </section>