--- a/bigwig_outlier_bed.xml	Sun Sep 15 17:08:45 2024 +0000
+++ b/bigwig_outlier_bed.xml	Mon Sep 30 01:42:34 2024 +0000
@@ -1,9 +1,9 @@
-<tool name="Bigwig extremes to bed features" id="bigwig_outlier_bed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
+<tool name="Bigwig outliers to bed features" id="bigwig_outlier_bed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
   <description>Writes high and low bigwig runs as features in a bed file</description>
   <macros>
   <token name="@TOOL_VERSION@">0.2.0</token>
   <token name="@PYTHON_VERSION@">3.12.3</token>
-  <token name="@VERSION_SUFFIX@">1</token>
+  <token name="@VERSION_SUFFIX@">2</token>
   </macros>
   <edam_topics>
       <edam_topic>topic_0157</edam_topic>
@@ -43,6 +43,9 @@
 #if $outbeds in ['outlo', 'outall', 'outlohi']:
   --bedoutlo '$bedoutlo'
 #end if
+#if $outbeds in ['outzero']:
+  --bedoutzero '$bedoutzero'
+#end if
 --minwin '$minwin'
 #if $qhi:
 --qhi '$qhi'
@@ -67,9 +70,10 @@
       <option value="outhilo" selected="true">Make 1 bed output with both low and high regions</option>
       <option value="outhi">Make 1 bed output with high regions only</option>
       <option value="outlo">Make 1 bed output with low regions only</option>
+      <option value="outzero">Make 1 bed output for regions with contiguous zero values only</option>
       <option value="outall">Make 3 bed outputs with low and high together in one, high in one and low in the other</option>
       <option value="outlohi">Make 2 bed outputs with high in one and low in the other</option>
-      <option value="outtab">NO bed outputs. Report bigwig value distribution only</option>
+      <option value="outtab">NO bed outputs. Report bigwig value distribution table only</option>
     </param>
     <param name="tableout" type="select" label="Write a table showing contig statistics for each bigwig input" help="">
       <option value="donotmake">Do not create this report</option>
@@ -86,6 +90,9 @@
     <data name="bedoutlo" format="bed" label="Low bed">
       <filter>outbeds in ["outall", "outlohi", "outlo"]</filter>
     </data>
+    <data name="bedoutzero" format="bed" label="Zeros only bed">
+      <filter>outbeds in ["outzero"]</filter>
+    </data>
     <data name="tableoutfile" format="txt" label="Contig statistics">
       <filter>tableout == "create" or outbeds == "outtab"</filter>
     </data>
@@ -150,9 +157,15 @@
       <param name="qlo" value="0.5"/>
       <param name="tableout" value="create"/>
     </test>
-
-
-
+    <test expect_num_outputs="1">
+      <output name="bedoutzero" value="bedoutzero_sample" compare="diff" lines_diff="0"/>
+      <param name="outbeds" value="outzero"/>
+      <param name="bigwig" value="fake.bigwig,bigwig_sample"/>
+      <param name="minwin" value="2"/>
+      <param name="qhi" value="0.5"/>
+      <param name="qlo" value="0.5"/>
+      <param name="tableout" value="donotmake"/>
+    </test>
   </tests>
   <help><![CDATA[