--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hal_halMaskExtract.xml	Fri Feb 06 10:33:04 2026 +0000
@@ -0,0 +1,84 @@
+<tool id="hal_halmaskextract" name="halMaskExtract" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>extracts masked intervals of a genome into BED file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/> 
+    <expand macro="stdio"/>
+    <command detect_errors="aggressive"><![CDATA[
+        halMaskExtract
+            #if $mode.regions == '--extend':
+                --extend $mode.extend
+            #else if $mode.regions == '--extendPct':
+                --extendPct $mode.extendPct
+            #end if
+            '$input_hal' '$refGenome' > '$out_file'
+    ]]></command>
+    <inputs>
+        <expand macro="input_hal"/>
+        <expand macro="params_refGenome"/>
+        <conditional name="mode">
+            <param name="regions" type="select" label="Extend masked regions">
+                <option value="" selected="true">No, don't extend</option>
+                <option value="--extend">Yes, extend by given number of bases (--extend)</option>
+                <option value="--extendPct">Yes, extend by percentage of their lengths (--extendPct)</option>
+            </param>
+            <when value=""/>
+            <when value="--extend">
+                <param name="extend" type="integer" min="0" value="0" label="Number of bases" help="Extend masked regions by given number of bases"/>
+            </when>
+            <when value="--extendPct">
+                <param name="extendPct" type="float" min="0" value="0" label="Percentage" help="Extend masked regions by percentage of their lengths"/>
+            </when>
+        </conditional>
+    </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="halTestIndels.hal"/>
+            <param name="refGenome" value="Ref"/>
+            <output name="out_file" ftype="bed">
+                <assert_contents>
+                    <has_line line="chr1&#009;5&#009;10"/>
+                    <has_n_lines n="1"/>
+                </assert_contents>    
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTestIndels.hal"/>
+            <param name="refGenome" value="Ref"/>
+            <conditional name="mode">
+                <param name="regions" value="--extend"/>
+                <param name="extend" value="100"/>
+            </conditional>
+            <output name="out_file" ftype="bed">
+                <assert_contents>
+                    <has_line line="chr1&#009;5&#009;100"/>
+                    <has_n_lines n="1"/>
+                </assert_contents> 
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTestIndels.hal"/>
+            <param name="refGenome" value="Ref"/>
+            <conditional name="mode">
+                <param name="regions" value="--extendPct"/>
+                <param name="extendPct" value="0.25"/>
+            </conditional>
+            <output name="out_file" ftype="bed">
+                <assert_contents>
+                    <has_line line="chr1&#009;4&#009;11"/>
+                    <has_n_lines n="1"/>
+                </assert_contents> 
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+halMaskExtract extracts masked regions from a given genome found in an input HAL file and writes them as BED intervals.
+Options let you extend intervals by a fixed number of bases or by a percentage of interval length.
+    ]]></help>
+    <expand macro="citation"/>
+    <expand macro="creator"/>
+</tool>
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