--- a/autogenJB2.xml	Sun Feb 25 04:18:53 2024 +0000
+++ b/autogenJB2.xml	Wed Feb 28 10:08:57 2024 +0000
@@ -1,5 +1,5 @@
- <tool id="autogenjb2" name="autogenjb2" version="2.10.0_0" profile="22.05">
-    <description>Files to JBrowse2</description>
+ <tool id="autogenjb2" name="autogenjb2" version="2.10.2_0" profile="22.05">
+    <description>Track collection to JBrowse2</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -11,20 +11,35 @@
     <version_command>python '${__tool_directory__}/autogenJB2.py' --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
 python '$__tool_directory__/autogenJB2.py'
-#for $key in $jbrowseme.keys():
---collection '$key,$jbrowseme[$key],$jbrowseme[$key].ext'
+#for $key in $autoCollection.keys():
+    #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'
+    #else if $autoCollection[$key].ext in ['bam',]
+      --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index'
+     #else if $autoCollection[$key].ext in ['cram',]
+      --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index'
+    #end if
 #end for
---sessName "Autogen JBrowse"
+--outdir '$output.files_path'
+--sessName "Autogen JBrowse" &&
+
+  cp '$output.files_path/index.html' '$output'
+
+## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
+
+
   ]]></command>
     <inputs>
         <param
-                    label="Collection of files specially named to become tracks"
-                    name="jbrowseme"
+                    label="Collection of files to become tracks - they must have short, informative names"
+                    name="autoCollection"
                     type="data_collection">
         </param>
     </inputs>
     <outputs>
-        <data format="html" name="output" label="JBrowse2"/>
+        <data format="html" name="output" label="AutoJBrowse2"/>
     </outputs>
 
     <help><![CDATA[