# HG changeset patch
# User iuc
# Date 1773846432 0
# Node ID 36cea1c55698926c011b17a652a538651b5e04b1
# Parent  48d453b8f39dc17685b2d9c7208d7df1ab4bfca6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 30ac0af6dfa729277011bcd73cd5560efa03fb97

diff -r 48d453b8f39d -r 36cea1c55698 hal_halCoverage.xml
--- a/hal_halCoverage.xml	Fri Feb 06 10:39:17 2026 +0000
+++ b/hal_halCoverage.xml	Wed Mar 18 15:07:12 2026 +0000
@@ -12,7 +12,7 @@
             --seed $seed
             $bySequence
             ## Pipes output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree.
-            '$input_hal' '$refGenome' | tr ',' '\t' > '$out_file' 
+            '$input_hal' '$refGenome' | sed $'s/, */\t/g' > '$out_file' 
     ]]></command>
     <inputs>
         <expand macro="input_hal"/>
@@ -31,8 +31,8 @@
             <param name="seed" value="100"/>
             <output name="out_file" ftype="tabular">
                 <assert_contents>
-                    <has_line line="Genome&#009; sitesCovered1Times&#009; sitesCovered2Times&#009; sitesCovered3Times&#009; sitesCovered4Times&#009; sitesCovered5Times"/>
-                    <has_line line="Genome_2&#009; 856475&#009; 482343&#009; 482343&#009; 214021&#009; 0"/>
+                    <has_line line="Genome&#009;sitesCovered1Times&#009;sitesCovered2Times&#009;sitesCovered3Times&#009;sitesCovered4Times&#009;sitesCovered5Times"/>
+                    <has_line line="Genome_2&#009;856475&#009;482343&#009;482343&#009;214021&#009;0"/>
                     <has_n_lines n="4"/>
                 </assert_contents>
             </output>
@@ -44,8 +44,8 @@
             <param name="seed" value="100"/>
             <output name="out_file" ftype="tabular">
                 <assert_contents>
-                    <has_line line="Genome&#009; sitesCovered1Times&#009; sitesCovered2Times&#009; sitesCovered3Times&#009; sitesCovered4Times&#009; sitesCovered5Times"/>
-                    <has_line line="Genome_2&#009; 839&#009; 500&#009; 500&#009; 233&#009; 0"/>
+                    <has_line line="Genome&#009;sitesCovered1Times&#009;sitesCovered2Times&#009;sitesCovered3Times&#009;sitesCovered4Times&#009;sitesCovered5Times"/>
+                    <has_line line="Genome_2&#009;839&#009;500&#009;500&#009;233&#009;0"/>
                     <has_n_lines n="4"/>
                 </assert_contents>
             </output>
@@ -57,8 +57,8 @@
             <param name="seed" value="100"/>
             <output name="out_file" ftype="tabular">
                 <assert_contents>
-                    <has_line line="Genome&#009; sitesCovered1Times&#009; sitesCovered2Times&#009; sitesCovered3Times&#009; sitesCovered4Times&#009; sitesCovered5Times"/>
-                    <has_line line="Genome_2&#009; 856475&#009; 482343&#009; 482343&#009; 214021&#009; 0"/>
+                    <has_line line="Genome&#009;sitesCovered1Times&#009;sitesCovered2Times&#009;sitesCovered3Times&#009;sitesCovered4Times&#009;sitesCovered5Times"/>
+                    <has_line line="Genome_2&#009;856475&#009;482343&#009;482343&#009;214021&#009;0"/>
                     <has_line line="Coverage on Genome_1_seq"/>
                     <has_n_lines n="9"/>
                 </assert_contents>
diff -r 48d453b8f39d -r 36cea1c55698 macros.xml
--- a/macros.xml	Fri Feb 06 10:39:17 2026 +0000
+++ b/macros.xml	Wed Mar 18 15:07:12 2026 +0000
@@ -4,8 +4,9 @@
             <requirement type="package" version="@TOOL_VERSION@">cactus</requirement>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">2.9.9</token>
+    <token name="@TOOL_VERSION@">3.1.4</token>
     <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX_HAL2VG@">1</token>
     <token name="@PROFILE@">25.1</token>
     <xml name="stdio">
         <stdio>
@@ -171,7 +172,7 @@
         <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>  
diff -r 48d453b8f39d -r 36cea1c55698 test-data/halAddToBranch_bot_input.hal
Binary file test-data/halAddToBranch_bot_input.hal has changed
diff -r 48d453b8f39d -r 36cea1c55698 test-data/halAddToBranch_top_input.hal
Binary file test-data/halAddToBranch_top_input.hal has changed
diff -r 48d453b8f39d -r 36cea1c55698 test-data/halTestExtended.hal
Binary file test-data/halTestExtended.hal has changed