--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hal_halAddToBranch.xml	Fri Feb 06 10:33:34 2026 +0000
@@ -0,0 +1,104 @@
+<tool id="hal_haladdtobranch" name="halAddToBranch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>adds a new internal node and leaf genome into an existing HAL </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 && 
+        halAddToBranch
+            $noMarkAncestors
+            writable_hal.hal '$botAlignmentFile' '$topAlignmentFile' '$parentName' '$insertName' '$childName' '$leafName' '$upperBranchLength' '$leafBranchLength' &&
+        ## echo 'ok' to check it with assert_stdout. This is needed because there is no other stdout output, 
+        ## and the output HAL file checksum always changes even with identical inputs.
+        echo 'ok'
+    ]]></command>
+    <inputs>
+        <expand macro="input_hal"/>
+        <param name="insertName" type="text" value="" label="Insert name" help="Name of the new internal node to be created. Must be present in both top and bottom alignment files">
+            <expand macro="sanitizer_default"/>
+            <expand macro="validator_trim"/>
+        </param>
+        <param name="parentName" type="text" value="" label="Parent name" help="Name of the existing genome in the main tree that will become the parent of the new insert node">
+            <expand macro="sanitizer_default"/>
+            <expand macro="validator_trim"/>
+        </param>
+        <param name="childName" type="text" value="" label="Child name" help="Name of the existing genome that is being moved. It will be detached from the parent and re-attached to the new insert">
+            <expand macro="sanitizer_default"/>
+            <expand macro="validator_trim"/>
+        </param>
+        <param name="leafName" type="text" value="" label="Leaf name" help="Name of the new leaf genome being added to the tree. Must be present in the bottom alignment file">
+            <expand macro="sanitizer_default"/>
+            <expand macro="validator_trim"/>
+        </param>
+        <param name="topAlignmentFile" type="data" format="hal" label="Top alignment file" help="HAL file defining the connection between the parent and the new insert. A tree containing the insert, its parent, and its siblings"/>
+        <param name="botAlignmentFile" type="data" format="hal" label="Bottom alignment file" help="HAL file defining the subtree starting from the new insert node. A tree containing the insert, its children, and its new leaf genome"/>
+        <param name="upperBranchLength" type="float" min="0" label="Upper branch length" help="Length of branch from parent to insert"/>
+        <param name="leafBranchLength" type="float" min="0" label="Leaf branch length" help="Leaf branch length"/>
+        <expand macro="params_noMarkAncestors"/>
+    </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="botAlignmentFile" value="halAddToBranch_bot_input.hal"/>
+            <param name="topAlignmentFile" value="halAddToBranch_top_input.hal"/>
+            <param name="parentName" value="Genome_0"/>
+            <param name="insertName" value="Insert"/>
+            <param name="childName" value="Genome_2"/>
+            <param name="leafName" value="NewLeaf"/>
+            <param name="upperBranchLength" value="1"/>
+            <param name="leafBranchLength" value="1"/>
+            <output name="out_file" ftype="hal">
+                <assert_contents>
+                    <has_size min="80000"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_line line="ok"/>
+            </assert_stdout>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="botAlignmentFile" value="halAddToBranch_bot_input.hal"/>
+            <param name="topAlignmentFile" value="halAddToBranch_top_input.hal"/>
+            <param name="parentName" value="Genome_0"/>
+            <param name="insertName" value="Insert"/>
+            <param name="childName" value="Genome_2"/>
+            <param name="leafName" value="NewLeaf"/>
+            <param name="upperBranchLength" value="1"/>
+            <param name="leafBranchLength" value="1"/>
+            <param name="noMarkAncestors" value="true"/>
+            <output name="out_file" ftype="hal">
+                <assert_contents>
+                    <has_size min="80000"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_line line="ok"/>
+            </assert_stdout>
+        </test>
+    </tests>
+    <help><![CDATA[
+halAddToBranch adds a new internal genome node and a new leaf genome to an input HAL alignment by splitting an existing branch. 
+A new internal node is inserted between a specified parent and child, and a new leaf genome is attached to that inserted node.
+Bottom and top alignment files are required to correctly connect the inserted node to its descendants and ancestors. 
+By default, ancestor nodes are marked for update to ensure consistency of the alignment after replacement. 
+This behavior can be disabled when ancestor updates are not required.
+
+A new HAL file is created as output instead of modifying the input HAL file.
+
+-----
+
+.. class:: warningmark
+
+Running the tool on a HAL file in mmap format will fail because this format type is not supported by this tool.
+It is recommended to convert the input to HDF5 format first using halExtract.
+    ]]></help>
+    <expand macro="citation"/>
+    <expand macro="creator"/>
+</tool>
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