--- a/autogenJB2.xml	Fri Mar 01 05:15:41 2024 +0000
+++ b/autogenJB2.xml	Mon Mar 04 09:47:19 2024 +0000
@@ -13,7 +13,17 @@
 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2  &&
 python '$__tool_directory__/autogenJB2.py'
 #for $key in $autoCollection.keys():
-    #if $autoCollection[$key].ext == 'fasta':
+    #if $autoCollection[$key].is_collection:
+        #set subCol=$autoCollection[$key]
+        #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf']
+        #if len($pafs) > 0:
+             --pafmeta '$pafs[0]'
+            #set refs = [($pafs[0][2],$subCol[x],x) for x in $subCol.keys() if $subCol[x].ext == 'fasta']
+            #for $ref in $refs:
+             --pafreferencemeta '$ref'
+            #end for
+        #end if
+    #else if $autoCollection[$key].ext == 'fasta':
       --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
     #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf']
       --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
@@ -45,23 +55,21 @@
         <data format="html" name="output" label="AutoJBrowse2"/>
     </outputs>
 <tests>
- <test>
+   <test>
       <param name="uglyTestingHack" value="enabled" />
       <param name="autoCollection">
         <collection type="list">
           <element name="Merlin" value="merlin.fa" ftype="fasta"/>
-          <element name="merlin-sample.bam" value="bam/merlin-sample.bam" ftype="bam"/>
+          <element name="test-6.bed" value="bed/test-6.bed" ftype="bed"/>
         </collection>
       </param>
-            <output name="output">
-                <assert_contents>
-                    <has_text text='"name": "Merlin",'/>
-                    <has_text text='"name": "merlin-sample.bam",'/>
-                    <has_text text='"uri": "Merlin.fa.gz.fai"'/>
-                    <has_text text='"uri": "bam_0_merlin-sample.bam.bam.bai"'/>
-
-                </assert_contents>
-            </output>
+      <output name="output">
+            <assert_contents>
+                <has_text text='"name": "Merlin",'/>
+                <has_text text='"name": "test-6.bed",'/>
+                <has_text text='"uri": "Merlin.fa.gz.fai"'/>
+            </assert_contents>
+      </output>
     </test>
 </tests>
     <help><![CDATA[