--- a/bigwig_outlier_bed.xml	Thu Jul 25 14:38:34 2024 +0000
+++ b/bigwig_outlier_bed.xml	Sun Sep 15 17:08:45 2024 +0000
@@ -3,7 +3,7 @@
   <macros>
   <token name="@TOOL_VERSION@">0.2.0</token>
   <token name="@PYTHON_VERSION@">3.12.3</token>
-  <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@VERSION_SUFFIX@">1</token>
   </macros>
   <edam_topics>
       <edam_topic>topic_0157</edam_topic>
@@ -25,13 +25,13 @@
   </required_files>
   <version_command><![CDATA[python -c "import pybigtools; from importlib.metadata import version; print(version('pybigtools'))"]]></version_command>
   <command><![CDATA[python '${__tool_directory__}/bigwig_outlier_bed.py'
---bigwig 
-#for bw in $bigwig: 
- '$bw' 
+#set bwns = [x.name for x in $bigwig]
+#set bwfs = [x for x in $bigwig]
+#for $bwf in $bwfs:
+--bigwig '$bwf'
 #end for
---bigwiglabels
-#for bw in $bigwig: 
-  '$bw.name'
+#for $bwn in $bwns:
+--bigwiglabels '$bwn'
 #end for
 --outbeds '$outbeds'
 #if $outbeds in ['outhilo', 'outall']:
@@ -94,29 +94,29 @@
     <test expect_num_outputs="1">
       <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/>
       <param name="outbeds" value="outhilo"/>
-      <param name="bigwig" value="bigwig_sample"/>
+      <param name="bigwig" value="fake.bigwig"/>
       <param name="minwin" value="10"/>
-      <param name="qhi" value="0.99"/>
+      <param name="qhi" value="0.6"/>
       <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="bigwig" value="fake.bigwig"/>
       <param name="minwin" value="10"/>
-      <param name="qhi" value="0.99"/>
-      <param name="qlo" value="0.01"/>
+      <param name="qhi" value="0.7"/>
+      <param name="qlo" value="0.3"/>
       <param name="tableout" value="create"/>
     </test>
     <test expect_num_outputs="2">
-      <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/>
+      <output name="bedouthilo" value="bedouthilo_sample_2" compare="diff" lines_diff="0"/>
       <output name="tableoutfile" value="table_sample" compare="diff" lines_diff="0"/>
       <param name="outbeds" value="outhilo"/>
       <param name="bigwig" value="bigwig_sample"/>
       <param name="minwin" value="10"/>
-      <param name="qhi" value="0.99"/>
-      <param name="qlo" value="0.01"/>
+      <param name="qhi" value="0.7"/>
+      <param name="qlo" value="0.3"/>
       <param name="tableout" value="create"/>
     </test>
     <test expect_num_outputs="2">
@@ -125,7 +125,7 @@
       <param name="outbeds" value="outhi"/>
       <param name="bigwig" value="bigwig_sample"/>
       <param name="minwin" value="10"/>
-      <param name="qhi" value="0.99"/>
+      <param name="qhi" value="0.69"/>
       <param name="qlo" value=""/>
       <param name="tableout" value="create"/>
     </test>
@@ -134,24 +134,25 @@
       <output name="bedoutlo" value="bedoutlo_sample" compare="diff" lines_diff="0"/>
       <output name="tableoutfile" value="table3_sample" compare="diff" lines_diff="0"/>
       <param name="outbeds" value="outlohi"/>
-      <param name="bigwig" value="bigwig_sample"/>
-      <param name="minwin" value="1"/>
-      <param name="qhi" value="0.9"/>
-      <param name="qlo" value="0.1"/>
+      <param name="bigwig" value="fake.bigwig"/>
+      <param name="minwin" value="10"/>
+      <param name="qhi" value="0.5"/>
+      <param name="qlo" value="0.5"/>
       <param name="tableout" value="create"/>
     </test>
-    <test expect_num_outputs="4">
-      <output name="bedouthilo" value="bedouthilo2_sample" compare="diff" lines_diff="0"/>
-      <output name="bedoutlo" value="bedoutlo2_sample" compare="diff" lines_diff="0"/>
+    <test expect_num_outputs="2">
       <output name="bedouthi" value="bedouthi2_sample" compare="diff" lines_diff="0"/>
       <output name="tableoutfile" value="table2_sample" compare="diff" lines_diff="0"/>
-      <param name="outbeds" value="outall"/>
-      <param name="bigwig" value="bigwig_sample,1.bigwig"/>
-      <param name="minwin" value="1"/>
-      <param name="qhi" value="0.9"/>
-      <param name="qlo" value="0.1"/>
+      <param name="outbeds" value="outhi"/>
+      <param name="bigwig" value="fake.bigwig,bigwig_sample"/>
+      <param name="minwin" value="10"/>
+      <param name="qhi" value="0.5"/>
+      <param name="qlo" value="0.5"/>
       <param name="tableout" value="create"/>
     </test>
+
+
+
   </tests>
   <help><![CDATA[