# HG changeset patch
# User iuc
# Date 1772710334 0
# Node ID 8af265f90d580362f801e2cf1ada377b4eec373e
# Parent  0cfe56c4ac6830f979b4bca806d767426c50f87c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit f46096b336bf460424143fc9d633b5e7c20bf1cf

diff -r 0cfe56c4ac68 -r 8af265f90d58 hal_maf2hal.xml
--- a/hal_maf2hal.xml	Fri Feb 06 10:45:54 2026 +0000
+++ b/hal_maf2hal.xml	Thu Mar 05 11:32:14 2026 +0000
@@ -12,12 +12,12 @@
             cp '$mode.input_hal' writable_hal.hal && 
         #end if
         ## Uncompress input
-        #if $input_maf.ext.endswith('.gz'):
+        #if $input_maf.is_of_type('maf.gz'):
             gunzip -c '$input_maf' > uncompressed_input.maf &&
-        #else if $input_maf.ext.endswith('.bz2'):
+        #else if $input_maf.is_of_type('maf.bz2'):
             bunzip2 -c '$input_maf' > uncompressed_input.maf &&
         #else
-            cp '$input_maf' uncompressed_input.maf &&
+            ln -s '$input_maf' uncompressed_input.maf &&
         #end if
         maf2hal
             #if $refGenome:
diff -r 0cfe56c4ac68 -r 8af265f90d58 macros.xml
--- a/macros.xml	Fri Feb 06 10:45:54 2026 +0000
+++ b/macros.xml	Thu Mar 05 11:32:14 2026 +0000
@@ -5,7 +5,7 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">2.9.9</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">25.1</token>
     <xml name="stdio">
         <stdio>
@@ -171,7 +171,7 @@
         <validator type="regex" message="Enter without leading or trailing spaces">^\S(?:.*\S)?$</validator>   
     </xml>
     <xml name="validator_comma_list">
-        <validator type="regex" message="Enter a comma separated list of genomes, without leading or trailing spaces">^\S(?:[^,]*\S)?(?:,\S(?:[^,]*\S)?)*$</validator>
+        <validator type="regex" message="Enter a comma separated list of genomes, without leading or trailing spaces">^[^,\s]+(,[^,\s]+)*$</validator>
     </xml>
     <xml name="validator_newick">
         <validator type="regex" message="Enter a Newick tree">^.*;$</validator>