--- a/bigwig_outlier_bed.xml	Sun Jul 21 11:03:36 2024 +0000
+++ b/bigwig_outlier_bed.xml	Thu Jul 25 14:38:34 2024 +0000
@@ -1,9 +1,9 @@
-<tool name="Bigwig extremes to bed features" id="bigwig_outlier_bed" version="@TOOL_VERSION@" profile="22.05">
+<tool name="Bigwig extremes 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="@NUMPY_VERSION@">2.0.0</token>
   <token name="@PYTHON_VERSION@">3.12.3</token>
+  <token name="@VERSION_SUFFIX@">0</token>
   </macros>
   <edam_topics>
       <edam_topic>topic_0157</edam_topic>
@@ -17,7 +17,7 @@
   </xrefs>
   <requirements>
     <requirement type="package" version="@PYTHON_VERSION@">python</requirement>
-    <requirement type="package" version="@NUMPY_VERSION@">numpy</requirement>
+    <requirement type="package" version="2.0.0">numpy</requirement>
     <requirement type="package" version="@TOOL_VERSION@">pybigtools</requirement>
   </requirements>
   <required_files>
@@ -50,7 +50,7 @@
 #if $qlo:
 --qlo '$qlo'
 #end if
-#if $tableout == "create":
+#if $tableout == "create" or $outbeds == "outtab":
  --tableoutfile '$tableoutfile'
 #end if
 ]]></command>
@@ -58,15 +58,18 @@
     <param name="bigwig" type="data" optional="false" label="Choose one or more bigwig file(s) to return outlier regions as a bed file" 
       help="If more than one, MUST all use the same reference sequence to be displayable. Feature names will include the bigwig label." format="bigwig" multiple="true"/>
     <param name="minwin" type="integer" value="10" label="Minimum continuous bases to count as a high or low bed feature" 
-      help="Continuous features as long or longer than this window size will appear as bed features"/>
-    <param name="qhi" type="float" value="0.99" label="Quantile cutoff for a high region - 0.99 will cut off at or above the 99th percentile" help="Required" optional="false"/>
-    <param name="qlo" type="float" value="0.01" label="Quantile cutoff for a low region - 0.01 will cut off at or below the 1st percentile." help="Optional" optional="true"/>
-    <param name="outbeds" type="select" label="Select the required bed file outputs" help="Any combination of the 3 different kinds of bed file output can be made">
+      help="Minimum continuous length to count as a bed feature. If windowed bigwig, must be bigger than window size to have any effect"/>
+    <param name="qhi" type="float" value="0.99999" label="Quantile cutoff for a high region - 0.99999 will cut off at about 1 in 100,000" 
+       help="1 per 100k might be a few thousand features in a 200M chromosome - depends on the distribution - see the table output" optional="false"/>
+    <param name="qlo" type="float" value="0.00001" label="Quantile cutoff for a low region - 0.01 will cut off at or below the 1st percentile." help="Optional" optional="true"/>
+    <param name="outbeds" type="select" label="Select the required bed file outputs or none for a bigwig value distribution report" 
+      help="Any combination of the 3 different kinds of bed file output can be made">
       <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="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>
     </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>
@@ -74,17 +77,17 @@
     </param>
   </inputs>
   <outputs>
-    <data name="bedouthilo" format="bed" label="High_and_low_bed" hidden="false">
+    <data name="bedouthilo" format="bed" label="High_and_low_bed">
       <filter>outbeds in ["outall", "outhilo"]</filter>
     </data>
-    <data name="bedouthi" format="bed" label="High bed" hidden="false">
+    <data name="bedouthi" format="bed" label="High bed">
       <filter>outbeds in ["outall", "outlohi", "outhi"]</filter>
     </data>
-    <data name="bedoutlo" format="bed" label="Low bed" hidden="false">
+    <data name="bedoutlo" format="bed" label="Low bed">
       <filter>outbeds in ["outall", "outlohi", "outlo"]</filter>
     </data>
-    <data name="tableoutfile" format="tabular" label="Contig statistics" hidden="false">
-      <filter>tableout == "create"</filter>
+    <data name="tableoutfile" format="txt" label="Contig statistics">
+      <filter>tableout == "create" or outbeds == "outtab"</filter>
     </data>
   </outputs>
   <tests>
@@ -97,6 +100,15 @@
       <param name="qlo" value="0.01"/>
       <param name="tableout" value="donotmake"/>
     </test>
+    <test expect_num_outputs="1">
+      <output name="tableoutfile" value="table_only_sample" compare="diff" lines_diff="0"/>
+      <param name="outbeds" value="outtab"/>
+      <param name="bigwig" value="bigwig_sample,1.bigwig"/>
+      <param name="minwin" value="10"/>
+      <param name="qhi" value="0.99"/>
+      <param name="qlo" value="0.01"/>
+      <param name="tableout" value="create"/>
+    </test>
     <test expect_num_outputs="2">
       <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/>
       <output name="tableoutfile" value="table_sample" compare="diff" lines_diff="0"/>