--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hal_hal2vg.xml	Fri Feb 06 10:37:20 2026 +0000
@@ -0,0 +1,122 @@
+<tool id="hal_hal2vg" name="hal2vg" version="1.1.8+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>converts HAL to a vg-compatible sequence graph</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="1.1.8">hal2vg</requirement>
+    </requirements>
+    <expand macro="stdio"/>
+    <command detect_errors="aggressive"><![CDATA[
+        hal2vg
+            #if $rootGenome:
+                --rootGenome '$rootGenome'
+            #end if
+            #if $mode.reference == '--refGenomes':
+                --refGenomes '$mode.refGenomes'
+            #end if
+            #if $selection.filter == '--targetGenomes':
+                --targetGenomes '$selection.targetGenomes'
+            #else if $selection.filter == '--ignoreGenomes':
+                --ignoreGenomes '$selection.ignoreGenomes'
+            #end if
+            #if $outputFormat == 'hg':
+                --outputFormat 'hg'
+            #end if
+            --chop $chop
+            $noAncestors
+            '$input_hal' > '$output_file'
+    ]]></command>
+    <inputs>
+        <expand macro="input_hal"/>
+        <conditional name="mode">
+            <param name="reference" type="select" label="Genomes to treat as reference paths" help="Specify genomes to treat as reference paths with all others as haplotype paths">
+                <option value="" selected="true">All genomes (default)</option>
+                <option value="--refGenomes">Specific reference genomes (--refGenomes)</option>
+            </param>
+            <when value=""/>
+            <when value="--refGenomes">
+                <param name="refGenomes" type="text" value="" label="List of genomes" help="Enter a comma-separated (no spaces) list of genomes to use as reference genomes">
+                    <expand macro="sanitizer_default"/>
+                    <expand macro="validator_comma_list"/>
+                </param>
+            </when>
+        </conditional>
+        <expand macro="params_rootGenome_optional"/>
+        <conditional name="selection">
+            <param name="filter" type="select" label="Genome selection filters">
+                <option value="" selected="true">All genomes (default)</option>
+                <option value="--targetGenomes">Specific genomes to target (--targetGenomes)</option>
+                <option value="--ignoreGenomes">Specific genomes to ignore (--ignoreGenomes)</option>
+            </param>
+            <when value=""/>
+            <when value="--targetGenomes">
+                <expand macro="params_targetGenomes"/>
+            </when>
+            <when value="--ignoreGenomes">
+                <param name="ignoreGenomes" type="text" value="" label="List of genome" help="Comma-separated (no spaces) list of genomes to ignore">
+                    <expand macro="sanitizer_default"/>
+                    <expand macro="validator_comma_list"/>
+                </param>
+            </when>
+        </conditional>
+        <param argument="--noAncestors" type="boolean" truevalue="--noAncestors" falsevalue="" checked="false" label="No ancestors" help="Don't write ancestral paths, nor sequence exclusive to ancestral genomes"/>
+        <param argument="--chop" type="integer" min="0" value="0" label="Chop" help="Chop up nodes in output graph so they are not longer than given length"/>
+        <param name="outputFormat" type="select" label="Output format">
+            <option value="pg" selected="true">pg (default)</option>
+            <option value="hg">hg</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="hal.pg" label="${tool.name} on ${on_string}: Graph">
+            <change_format>
+                <when input="outputFormat" value="hg" format="hal.hg"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <output name="output_file" ftype="hal.pg" file="hal2vg_output.pg"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="outputFormat" value="hg"/>
+            <output name="output_file" ftype="hal.hg" file="hal2vg_output.hg"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="rootGenome" value="Genome_0"/>
+            <conditional name="mode">
+                <param name="reference" value="--refGenomes"/>
+                <param name="refGenomes" value="Genome_0,Genome_1"/>
+            </conditional>
+            <output name="output_file" ftype="hal.pg" file="hal2vg_refGenomes_output.pg"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="noAncestors" value="true"/>
+            <output name="output_file" ftype="hal.pg" file="hal2vg_noAncestors_output.pg"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <conditional name="selection">
+                <param name="filter" value="--targetGenomes"/>
+                <param name="targetGenomes" value="Genome_0,Genome_1"/>
+            </conditional>
+            <param name="chop" value="10"/>
+            <output name="output_file" ftype="hal.pg" file="hal2vg_targetGenomes_chop_output.pg"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+hal2vg converts a HAL file to a vg-compatible sequence graph.
+The tool generates a graph representation where genomes can be treated as reference paths or haplotypes, optionally excluding ancestral sequences or selected genomes. 
+Control node length via chopping, select target or reference genomes, and choose the output format (PG or HG). 
+
+Use it for constructing genome graphs for downstream analyses such as variant calling, pangenome visualization, or graph-based mapping.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1038/s41587-023-01793-w</citation>
+    </citations>
+    <expand macro="creator"/>
+</tool>
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