--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hal_halSummarizeMutations.xml	Fri Feb 06 10:34:07 2026 +0000
@@ -0,0 +1,79 @@
+<tool id="hal_halsummarizemutations" name="halSummarizeMutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>creates a summary table of mutation events in the alignmet</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/> 
+    <expand macro="stdio"/>
+    <command detect_errors="aggressive"><![CDATA[
+        set -o pipefail; ## Sets the pipeline’s exit code to halSummarizeMutations’s on failure.
+        halSummarizeMutations
+            #if $mode.option == '--rootGenome':
+                --rootGenome '$mode.rootGenome'
+            #else if $mode.option == '--targetGenomes':
+                --targetGenomes '$mode.targetGenomes'
+            #end if
+            --maxGap $maxGap
+            --maxNFraction $maxNFraction
+            $justSubs
+            ## Pipes output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree.
+            '$input_hal' | tr ',' '\t' > '$output_file' 
+    ]]></command>
+    <inputs>
+        <expand macro="input_hal"/>
+        <conditional name="mode">
+            <param name="option" type="select" label="Summarize options">
+                <option value="" selected="true">All genomes (default)</option>
+                <option value="--targetGenomes">Specific target genomes (--targetGenomes)</option>
+                <option value="--rootGenome">Only genomes in a root genome subtree (--rootGenome)</option>
+            </param>
+            <when value=""/>
+            <when value="--rootGenome">
+                <expand macro="params_rootGenome"/>
+            </when>
+            <when value="--targetGenomes">
+                <expand macro="params_targetGenomes"/>
+            </when>
+        </conditional>
+        <expand macro="params_maxGap"/>
+        <expand macro="params_maxNFraction"/>
+        <param argument="--justSubs" type="boolean" truevalue="--justSubs" falsevalue="" checked="false" label="Just count substitutions" help="Results are total substitutions between genome and all children, rather than branch results. For tuning and performance checking only"/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Mutation events"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <output name="output_file" ftype="tabular">
+                <assert_contents>
+                    <has_text text="GenomeName&#009; ParentName&#009; BranchLength"/>
+                    <has_line line="Total&#009; &#009;3&#009; 15881&#009; 5274&#009; 0&#009; 0&#009; 0&#009; 12929&#009; 0&#009; 0&#009; 0&#009; 0&#009; 6&#009; 1304&#009; 0&#009; 0&#009; 0&#009; 0&#009; 28&#009; 8827&#009; 3&#009; 879&#009; 0"/>
+                    <has_n_lines n="8"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <conditional name="mode">
+                <param name="option" value="--rootGenome"/>
+                <param name="rootGenome" value="Genome_1"/>
+            </conditional>
+            <param name="justSubs" value="true"/>
+            <output name="output_file" ftype="tabular">
+                 <assert_contents>
+                    <has_text text="GenomeName&#009; ParentName&#009; BranchLength"/>
+                    <has_line line="Total&#009; &#009;3&#009; 17639&#009; 5274&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0"/>
+                    <has_n_lines n="9"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+halSummarizeMutations needs a HAL file as input and outputs a table that reports substitutions, indels, and other rearrangements across the alignment. 
+Focus the summary on selected genomes, a specific root genome, or the entire file. 
+The tool offers controls for how gaps and N rich regions are treated, and it can switch to a substitutions only mode for tuning and performance checking only. 
+    ]]></help>
+    <expand macro="citation"/>
+    <expand macro="creator"/>
+</tool>
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