# HG changeset patch
# User iuc
# Date 1772710242 0
# Node ID a9eb29f924e1243093a8639fc8bceaa351cfc5a9
# Parent  a9c52b2edba79398aecdfad8a90fa7634d22c351
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit f46096b336bf460424143fc9d633b5e7c20bf1cf

diff -r a9c52b2edba7 -r a9eb29f924e1 hal_halStats.xml
--- a/hal_halStats.xml	Fri Feb 06 10:48:53 2026 +0000
+++ b/hal_halStats.xml	Thu Mar 05 11:30:42 2026 +0000
@@ -7,11 +7,11 @@
     <expand macro="stdio"/>
     <command detect_errors="aggressive"><![CDATA[
         set -o pipefail; ## Sets the pipeline’s exit code to halStats’s on failure.
-        ( ## echo headers for specific numerical data
+        ## echo headers for specific numerical data
         #if $mode.option == '--baseComp':
-            echo -e 'fraction_of_As\tfraction_of_Gs\tfraction_of_Cs\tfraction_of_Ts';
+            echo -e 'fraction_of_As\tfraction_of_Gs\tfraction_of_Cs\tfraction_of_Ts' >> '$out_file' &&
         #else if $mode.option == '--numSegments':
-            echo -e 'numTopSegments\tnumBottomSegments';
+            echo -e 'numTopSegments\tnumBottomSegments' >> '$out_file' &&
         #end if
         halStats
             #if $mode.option == '--allCoverage':
@@ -60,13 +60,13 @@
                 --topSegments '$mode.topSegments'
             #end if
             '$input_hal'
-        ## Pipes specific output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree.
-        #if $mode.option == '--allCoverage' or $mode.option == '--sequenceStats' or $mode.option == '--percentID' or $mode.option == '--coverage':
-            | tr ',' '\t'
-        #else if $mode.option == '--numSegments':
-            | tr ' ' '\t' ## Replace spaces
-        #end if
-        ) > '$out_file'
+            ## Pipes specific output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree.
+            #if $mode.option == '--allCoverage' or $mode.option == '--sequenceStats' or $mode.option == '--percentID' or $mode.option == '--coverage':
+                | tr ',' '\t'
+            #else if $mode.option == '--numSegments':
+                | tr ' ' '\t' ## Replace spaces
+            #end if
+            >> '$out_file'
     ]]></command>
     <inputs>
         <expand macro="input_hal"/>
diff -r a9c52b2edba7 -r a9eb29f924e1 macros.xml
--- a/macros.xml	Fri Feb 06 10:48:53 2026 +0000
+++ b/macros.xml	Thu Mar 05 11:30:42 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>