--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hal_halRenameSequences.xml	Fri Feb 06 10:37:36 2026 +0000
@@ -0,0 +1,61 @@
+<tool id="hal_halrenamesequences" name="halRenameSequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>renames sequences of a genome in a HAL file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/> 
+    <expand macro="stdio"/>
+    <command detect_errors="aggressive"><![CDATA[
+        ## Copy input HAL to ensure that it is not modified.
+        cp '$input_hal' writable_hal.hal && 
+        halRenameSequences
+            writable_hal.hal '$refGenome' '$input_mapping'
+    ]]></command>
+    <inputs>
+        <expand macro="input_hal"/>
+        <expand macro="params_refGenome"/>
+        <expand macro="input_mapping"/>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="hal" label="${tool.name} on ${on_string}" from_work_dir="writable_hal.hal"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="refGenome" value="Genome_1"/>
+            <param name="input_mapping" value="halRenameSequences_input.txt"/>
+            <output name="out_file" ftype="hal">
+                <assert_contents>
+                    <has_size min="50000"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_line line="Renaming Genome_1_seq to Genome_test_1_seq"/>
+            </assert_stdout>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="refGenome" value="Genome_1"/>
+            <param name="input_mapping" value="halRenameSequences_input.tsv"/>
+            <output name="out_file" ftype="hal">
+                <assert_contents>
+                    <has_size min="50000"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_line line="Renaming Genome_1_seq to Genome_test_1_seq"/>
+            </assert_stdout>
+        </test>
+    </tests>
+    <help><![CDATA[
+halRenameSequences renames sequence names for a given reference genome from an input HAL file. 
+Sequence names are updated according to an input tab-separated mapping file. 
+Each row specifies an old sequence name and its corresponding new name.
+Only sequences listed in the mapping file are renamed. 
+All other sequence names in the given reference genome remain unchanged.
+
+A new HAL file is created as output instead of modifying the input HAL file.
+    ]]></help>
+    <expand macro="citation"/>
+    <expand macro="creator"/>
+</tool>
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