--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hal_halAlignedExtract.xml	Fri Feb 06 10:36:30 2026 +0000
@@ -0,0 +1,57 @@
+<tool id="hal_halalignedextract" name="halAlignedExtract" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>extracts aligned regions of a genome with its parent</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/> 
+    <expand macro="stdio"/>
+    <command detect_errors="aggressive"><![CDATA[
+        halAlignedExtract
+            $complement
+            $viewParentCoords
+            '$input_hal' '$genome' > '$out_file'
+    ]]></command>
+    <inputs>
+        <expand macro="input_hal"/>
+        <expand macro="params_genomeNoRoot"/>
+        <param argument="--viewParentCoords" type="boolean" truevalue="--viewParentCoords" falsevalue="" checked="false" label="View parent coordinates" help="View the corresponding parent coordinates for aligned regions"/>
+        <param argument="--complement" type="boolean" truevalue="--complement" falsevalue="" checked="false" label="Complement regions" help="Extract the regions of the genome that are *unaligned* to the parent. i.e. all intervals that are not returned with the default setting"/>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="bed" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="genome" value="Genome_1"/>
+            <param name="viewParentCoords" value="true"/>
+            <output name="out_file" ftype="bed">
+                <assert_contents>
+                    <has_line line="Genome_1_seq&#009;0&#009;293&#009;Genome_0_seq&#009;0&#009;293&#009;+"/>   
+                    <has_line line="Genome_1_seq&#009;2637&#009;2930&#009;Genome_0_seq&#009;293&#009;586&#009;+"/>    
+                    <has_line line="Genome_1_seq&#009;5135&#009;5274&#009;Genome_0_seq&#009;1033&#009;1172&#009;+"/>
+                    <has_n_lines n="26"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="genome" value="Genome_1"/>
+            <param name="complement" value="true"/>
+            <output name="out_file" ftype="bed">
+                <assert_contents>
+                    <has_line line="Genome_1_seq&#009;1465&#009;1758"/>   
+                    <has_line line="Genome_1_seq&#009;5274&#009;5472"/>
+                    <has_n_lines n="4"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+halAlignedExtract scans a given genome from an input HAL file and extracts regions that are aligned to its direct parent genome. 
+The tool reports all aligned blocks by default. Optionally, it can report the complementary set of regions that are not aligned to the parent.
+The output is written as BED intervals.
+    ]]></help>
+    <expand macro="citation"/>
+    <expand macro="creator"/>
+</tool>
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