--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hal_halIndels.xml	Fri Feb 06 10:34:53 2026 +0000
@@ -0,0 +1,67 @@
+<tool id="hal_halindels" name="halIndels" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>counts indels in the branch above the genome</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/> 
+    <expand macro="stdio"/>
+    <command detect_errors="aggressive"><![CDATA[
+        halIndels
+            --adjacentBases $adjacentBases
+            $onlyExtantTargets
+            '$input_hal' '$genome' > '$out_file'
+    ]]></command>
+    <inputs>
+        <expand macro="input_hal"/>
+        <expand macro="params_genomeNoRoot"/>
+        <param argument="--adjacentBases" type="integer" min="1" value="5" label="Adjacent bases" help="Number of adjacent bases to examine while filtering"/>
+        <param argument="--onlyExtantTargets" type="boolean" truevalue="--onlyExtantTargets" falsevalue="" checked="false" label="Only extant targets" help="Use only extant genomes for 'sibling'/outgroup"/>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="bed" label="${tool.name} on ${on_string}: Indel count"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTestIndels.hal"/>
+            <param name="genome" value="Ref"/>
+            <output name="out_file" ftype="bed">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                    <has_line line="chr1&#009;10&#009;10&#009;D&#009;5"/>
+                    <has_line line="# num sites possible: 25"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTestIndels.hal"/>
+            <param name="genome" value="Ref"/>
+            <param name="onlyExtantTargets" value="true"/>
+            <output name="out_file" ftype="bed">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                    <has_line line="chr1&#009;10&#009;10&#009;D&#009;5"/>
+                    <has_line line="# num sites possible: 25"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTestIndels.hal"/>
+            <param name="genome" value="Ref"/>
+            <param name="adjacentBases" value="10"/>
+            <output name="out_file" ftype="bed">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                    <has_line line="chr1&#009;10&#009;10&#009;D&#009;5"/>
+                    <has_line line="# num sites possible: 20"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+halIndels counts insertion and deletions on the branch above a given reference genome of an input HAL file and outputs the result as a BED file.
+The reference genome must not be the root of the alignment.
+Filtering can applied using a configurable number of adjacent bases to reduce noise.
+    ]]></help>
+    <expand macro="citation"/>
+    <expand macro="creator"/>
+</tool>
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