# HG changeset patch
# User iuc
# Date 1568209236 14400
# Node ID 9de82b4963e64b9e47ad46869eefbff13e8af156
# Parent  0ae74c70b267f6f769ce20e2fa5399a461f33f46
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"

diff -r 0ae74c70b267 -r 9de82b4963e6 jbrowse.py
--- a/jbrowse.py	Fri Aug 30 03:36:39 2019 -0400
+++ b/jbrowse.py	Wed Sep 11 09:40:36 2019 -0400
@@ -654,7 +654,8 @@
         # Only index if not already done
         if not os.path.exists(dest):
             cmd = ['sort', '-k1,1', '-k2,2n', data]
-            self.subprocess_check_call(cmd, output=dest)
+            with open(dest, 'w') as handle:
+                self.subprocess_check_call(cmd, output=handle)
 
             self.subprocess_check_call(['bgzip', '-f', dest])
             self.subprocess_check_call(['tabix', '-f', '-p', 'bed', dest + '.gz'])
diff -r 0ae74c70b267 -r 9de82b4963e6 jbrowse.xml
--- a/jbrowse.xml	Fri Aug 30 03:36:39 2019 -0400
+++ b/jbrowse.xml	Wed Sep 11 09:40:36 2019 -0400
@@ -673,6 +673,23 @@
       <param name="gencode" value="11" />
       <param name="standalone" value="Data Directory" />
       <repeat name="track_groups">
+        <param name="category" value="Default" />
+        <repeat name="data_tracks">
+            <conditional name="data_format">
+                <param name="data_format_select" value="gene_calls"/>
+                <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/>
+            </conditional>
+        </repeat>
+      </repeat>
+      <param name="uglyTestingHack" value="enabled" />
+      <output name="output" file="bed/test.xml" lines_diff="32"/>
+    </test>
+    <test>
+      <param name="reference_genome|genome_type_select" value="history"/>
+      <param name="reference_genome|genome" value="merlin.fa"/>
+      <param name="gencode" value="11" />
+      <param name="standalone" value="Data Directory" />
+      <repeat name="track_groups">
         <param name="category" value="Auto Coloured" />
         <repeat name="data_tracks">
             <conditional name="data_format">
@@ -861,7 +878,7 @@
       </repeat>
 
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gff3/test.xml" lines_diff="170" />
+      <output name="output" file="gff3/test.xml" lines_diff="240" />
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
diff -r 0ae74c70b267 -r 9de82b4963e6 macros.xml
--- a/macros.xml	Fri Aug 30 03:36:39 2019 -0400
+++ b/macros.xml	Wed Sep 11 09:40:36 2019 -0400
@@ -14,7 +14,7 @@
     </requirements>
   </xml>
   <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
-  <token name="@WRAPPER_VERSION@">galaxy4</token>
+  <token name="@WRAPPER_VERSION@">galaxy5</token>
   <token name="@ATTRIBUTION@"><![CDATA[
 **Attribution**
 
diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/bam/test.xml
--- a/test-data/bam/test.xml	Fri Aug 30 03:36:39 2019 -0400
+++ b/test-data/bam/test.xml	Wed Sep 11 09:40:36 2019 -0400
@@ -3,13 +3,13 @@
     <metadata>
         <gencode>11</gencode>
         <genomes>
-              <genome path="/tmp/tmpWtvfKr/files/000/dataset_20.dat">
+              <genome path="/tmp/tmpqkd9zdgq/files/d/3/d/dataset_d3d20b83-6a77-4e76-bb7e-3b9fe7261453.dat">
                 <metadata>
-                  <dataset id="b28067233c6d9fa0" hid="1"
+                  <dataset id="238993350abc9bfd" hid="1"
                       size="171.6 KB"
                       edam_format="format_1929"
                       file_ext="fasta" />
-                  <history id="fa6d20d0fb68383f"
+                  <history id="a90a30fafe298e1e"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -42,13 +42,13 @@
     <tracks>
         <track cat="Auto Coloured" format="pileup" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_21.dat" ext="bam" label="merlin-sample.bam">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/6/a/0/dataset_6a00d93a-ee34-42d5-897b-9470d6c71e1f.dat" ext="bam" label="merlin-sample.bam">
                 <metadata>
-                  <dataset id="c18708cec3343c17" hid="2"
+                  <dataset id="adba32ec9811aba7" hid="2"
                       size="12.9 KB"
                       edam_format="format_2572"
                       file_ext="bam" />
-                  <history id="fa6d20d0fb68383f"
+                  <history id="a90a30fafe298e1e"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -56,12 +56,10 @@
                       dbkey="?"
                       bam_version="1.3"
                       sort_order="coordinate"
-                      reference_names="[SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f62008d8a70 on: u__sq__Merlin__sq__]"
+                      reference_names="[SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f3deb10ba10 on: u__sq__Merlin__sq__]"
                       reference_lengths="[172788]"
-                      bam_header="{SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f62006f0a10 on: u__sq__SQ__sq__: [{SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f62006f0d70 on: u__sq__LN__sq__: 172788, SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f62006f0f50 on: u__sq__SN__sq__: SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200fe0470 on: u__sq__Merlin__sq__}], SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200fe0b90 on: u__sq__PG__sq__: [{SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200fe07d0 on: u__sq__PN__sq__: SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200fe0d10 on: u__sq__minimap2__sq__, SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200fe0590 on: u__sq__ID__sq__: SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200fe0cb0 on: u__sq__minimap2__sq__, SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200fe03b0 on: u__sq__VN__sq__: SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200fe0ad0 on: u__sq__2.5-r572__sq__, SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200fe0e90 on: u__sq__CL__sq__: SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200fe00b0 on: u__sq__minimap2 -a -x sr -t 1 reference.fa /net/datasrv3hs.sanbi.ac.za/datastore/cip0/software/galaxy/galaxy-ctb/galaxy/database/files/004/dataset_4697.dat__sq__}], SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200fe0a10 on: u__sq__HD__sq__: {SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200fe0830 on: u__sq__SO__sq__: SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200fe0350 on: u__sq__coordinate__sq__, SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200fe0e30 on: u__sq__VN__sq__: SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f62008d10b0 on: u__sq__1.3__sq__}}"
                       columns="12"
-                      column_names="[SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95f18 on: __sq__QNAME__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e958e8 on: __sq__FLAG__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e957e0 on: __sq__RNAME__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95b50 on: __sq__POS__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95788 on: __sq__MAPQ__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95730 on: __sq__CIGAR__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95d60 on: __sq__MRNM__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95d08 on: __sq__MPOS__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95c58 on: __sq__ISIZE__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e952b8 on: __sq__SEQ__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95418 on: __sq__QUAL__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95998 on: __sq__OPT__sq__]"
-                      bam_index="__lt__galaxy.model.MetadataFile object at 0x7f6200f6d1d0__gt__"
+                      bam_index="__lt__galaxy.model.MetadataFile(1) at 0x7f3de95da7d0__gt__"
                       />
                   <tool
                       tool_id="upload1"
@@ -78,7 +76,7 @@
                 <pileup>
                     <auto_snp>false</auto_snp>
                     <bam_indices>
-                        <bam_index>/tmp/tmpWtvfKr/files/_metadata_files/000/metadata_1.dat</bam_index>
+                        <bam_index>/tmp/tmpqkd9zdgq/files/_metadata_files/a/5/2/metadata_a520581b-e8cc-43e5-8514-3379cd5eaafb.dat</bam_index>
                     </bam_indices>
                     <chunkSizeLimit>5000000</chunkSizeLimit>
                 </pileup>
diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/bed/test-3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed/test-3.bed	Wed Sep 11 09:40:36 2019 -0400
@@ -0,0 +1,3 @@
+Merlin	49	1452
+Merlin	1457	2557
+Merlin	2557	3630
diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/bed/test-6.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed/test-6.bed	Wed Sep 11 09:40:36 2019 -0400
@@ -0,0 +1,3 @@
+Merlin	49	1452	chromosomal_replication_initiator_protein_DnaA	0	+
+Merlin	1457	2557	DNA_polymerase_III_subunit_beta	0	+
+Merlin	2557	3630	DNA_replication_and_repair_protein_RecF	0	+
diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/bed/test.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed/test.xml	Wed Sep 11 09:40:36 2019 -0400
@@ -0,0 +1,136 @@
+<?xml version="1.0"?>
+<root>
+    <metadata>
+        <gencode>11</gencode>
+        <genomes>
+              <genome path="/tmp/tmpqkd9zdgq/files/2/3/a/dataset_23ae18d3-c882-4d06-a36e-5a061da14b2e.dat">
+                <metadata>
+                  <dataset id="7b55dbb89df8f4e5" hid="1"
+                      size="171.6 KB"
+                      edam_format="format_1929"
+                      file_ext="fasta" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="?"
+                      data_lines="2881"
+                      sequences="1"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.6"
+                      />
+                </metadata>
+              </genome>
+        </genomes>
+        <general>
+            <defaultLocation></defaultLocation>
+            <trackPadding>20</trackPadding>
+
+            <shareLink>true</shareLink>
+            <aboutDescription></aboutDescription>
+            <show_tracklist>true</show_tracklist>
+            <show_nav>true</show_nav>
+            <show_overview>true</show_overview>
+            <show_menu>true</show_menu>
+            <hideGenomeOptions>false</hideGenomeOptions>
+        </general>
+        <galaxyUrl>http://localhost</galaxyUrl>
+    </metadata>
+    <tracks>
+        <track cat="Default" format="gene_calls" visibility="default_off">
+            <files>
+              <trackFile path="/tmp/tmpqkd9zdgq/files/1/0/3/dataset_103bde9a-c404-441e-99fc-cfaeb674e4ef.dat" ext="bed" label="test-3.bed">
+                <metadata>
+                  <dataset id="fa6d20d0fb68383f" hid="2"
+                      size="49 bytes"
+                      edam_format="format_3003"
+                      file_ext="bed" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="?"
+                      data_lines="3"
+                      columns="3"
+                      delimiter="__tc__"
+                      chromCol="1"
+                      startCol="2"
+                      endCol="3"
+                      viz_filter_cols="[4]"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.6"
+                      />
+                </metadata>
+              </trackFile>
+              <trackFile path="/tmp/tmpqkd9zdgq/files/d/e/1/dataset_de110c59-5762-4148-ba67-f3571280eae6.dat" ext="bed" label="test-6.bed">
+                <metadata>
+                  <dataset id="683bc220e21425bb" hid="3"
+                      size="180 bytes"
+                      edam_format="format_3003"
+                      file_ext="bed" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="?"
+                      data_lines="3"
+                      columns="6"
+                      delimiter="__tc__"
+                      chromCol="1"
+                      startCol="2"
+                      endCol="3"
+                      strandCol="6"
+                      nameCol="4"
+                      viz_filter_cols="[4]"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.6"
+                      />
+                </metadata>
+              </trackFile>
+            </files>
+
+            <options>
+                <style>
+                    <overridePlugins>False</overridePlugins>
+                    <overrideDraggable>False</overrideDraggable>
+                    <className>feature</className>
+                    <description>note,description</description>
+                    <label>product,name,id</label>
+                    <height>10px</height>
+                    <maxHeight>600</maxHeight>
+                </style>
+                <scaling>
+                        <method>ignore</method>
+                        <scheme>
+                            <color>__auto__</color>
+                        </scheme>
+                </scaling>
+                <menus>
+                </menus>
+                <custom_config>
+                </custom_config>
+
+                <gff>
+                    <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
+                    <index>false</index>
+                </gff>
+            </options>
+        </track>
+    </tracks>
+    <plugins
+        ComboTrackSelector=""
+        Bookmarks=""
+        GCContent=""
+        BlastView="True"
+        theme=""
+        />
+</root>
diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/custom_config/test.xml
--- a/test-data/custom_config/test.xml	Fri Aug 30 03:36:39 2019 -0400
+++ b/test-data/custom_config/test.xml	Wed Sep 11 09:40:36 2019 -0400
@@ -3,13 +3,13 @@
     <metadata>
         <gencode>11</gencode>
         <genomes>
-              <genome path="/tmp/tmpWtvfKr/files/000/dataset_17.dat">
+              <genome path="/tmp/tmpqkd9zdgq/files/1/a/7/dataset_1a77d084-9f64-48b9-802b-787e0e86c7b1.dat">
                 <metadata>
-                  <dataset id="27ee89e2e3d631e0" hid="1"
+                  <dataset id="a1e670e1ea0da54b" hid="1"
                       size="171.6 KB"
                       edam_format="format_1929"
                       file_ext="fasta" />
-                  <history id="7b55dbb89df8f4e5"
+                  <history id="683bc220e21425bb"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -42,13 +42,13 @@
     <tracks>
         <track cat="With custom track config" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_18.dat" ext="gff3" label="1.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/a/4/a/dataset_a4a9adc4-f3d3-4c05-8074-69e01ace1c78.dat" ext="gff3" label="1.gff">
                 <metadata>
-                  <dataset id="61f03d5eef6f1538" hid="2"
+                  <dataset id="9a22496ee796fbfc" hid="2"
                       size="2.3 KB"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="7b55dbb89df8f4e5"
+                  <history id="683bc220e21425bb"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -72,7 +72,7 @@
                 <style>
                     <overridePlugins>False</overridePlugins>
                     <overrideDraggable>False</overrideDraggable>
-                    <className>feature2</className>
+                    <className>feature</className>
                     <description>note,description</description>
                     <label>product,name,id</label>
                     <height>10px</height>
@@ -103,7 +103,6 @@
 
                 <gff>
                     <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <topLevelFeatures>mRNA</topLevelFeatures>
                     <index>false</index>
                 </gff>
             </options>
diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/endpoints/test.xml
--- a/test-data/endpoints/test.xml	Fri Aug 30 03:36:39 2019 -0400
+++ b/test-data/endpoints/test.xml	Wed Sep 11 09:40:36 2019 -0400
@@ -3,13 +3,13 @@
     <metadata>
         <gencode>11</gencode>
         <genomes>
-              <genome path="/tmp/tmpdcb31B/files/000/dataset_24.dat">
+              <genome path="/tmp/tmpqkd9zdgq/files/9/5/5/dataset_955a2615-e4c3-4ccc-ae7b-749a589abc12.dat">
                 <metadata>
-                  <dataset id="a1e670e1ea0da54b" hid="1"
+                  <dataset id="27a22803849b1486" hid="1"
                       size="171.6 KB"
                       edam_format="format_1929"
                       file_ext="fasta" />
-                  <history id="a90a30fafe298e1e"
+                  <history id="5449172d6ff5669b"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/gencode/test-1.xml
--- a/test-data/gencode/test-1.xml	Fri Aug 30 03:36:39 2019 -0400
+++ b/test-data/gencode/test-1.xml	Wed Sep 11 09:40:36 2019 -0400
@@ -3,7 +3,7 @@
     <metadata>
         <gencode>1</gencode>
         <genomes>
-              <genome path="/tmp/tmpZA6JJa/files/000/dataset_1.dat">
+              <genome path="/tmp/tmpqkd9zdgq/files/3/1/2/dataset_312987c8-262b-4b83-b9b1-9e6e84c6bee0.dat">
                 <metadata>
                   <dataset id="2891970512fa2d5a" hid="1"
                       size="171.6 KB"
diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/gencode/test-data_table.xml
--- a/test-data/gencode/test-data_table.xml	Fri Aug 30 03:36:39 2019 -0400
+++ b/test-data/gencode/test-data_table.xml	Wed Sep 11 09:40:36 2019 -0400
@@ -3,7 +3,7 @@
     <metadata>
         <gencode>1</gencode>
         <genomes>
-              <genome path="/home/abretaud/iuc_tools_abretaud/tools/jbrowse/test-data/merlin.fa">
+              <genome path="/home/hxr/arbeit/tools-iuc/tools/jbrowse/test-data/merlin.fa">
                   <metadata />
               </genome>s
         </genomes>
@@ -19,7 +19,7 @@
             <show_menu>true</show_menu>
             <hideGenomeOptions>false</hideGenomeOptions>
         </general>
-        <galaxyUrl>http://localhost:8080</galaxyUrl>
+        <galaxyUrl>http://localhost</galaxyUrl>
     </metadata>
     <tracks>
     </tracks>
diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/gencode/test.xml
--- a/test-data/gencode/test.xml	Fri Aug 30 03:36:39 2019 -0400
+++ b/test-data/gencode/test.xml	Wed Sep 11 09:40:36 2019 -0400
@@ -3,7 +3,7 @@
     <metadata>
         <gencode>11</gencode>
         <genomes>
-              <genome path="/tmp/tmpZA6JJa/files/000/dataset_3.dat">
+              <genome path="/tmp/tmpqkd9zdgq/files/8/b/1/dataset_8b116bbb-35ee-4d30-8d2d-ee31d8b49228.dat">
                 <metadata>
                   <dataset id="54f2a3a23292eb07" hid="1"
                       size="171.6 KB"
diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/gff3/test.xml
--- a/test-data/gff3/test.xml	Fri Aug 30 03:36:39 2019 -0400
+++ b/test-data/gff3/test.xml	Wed Sep 11 09:40:36 2019 -0400
@@ -3,13 +3,13 @@
     <metadata>
         <gencode>11</gencode>
         <genomes>
-              <genome path="/tmp/tmpTx5wXw/files/000/dataset_5.dat">
+              <genome path="/tmp/tmpqkd9zdgq/files/b/f/a/dataset_bfad32fe-cc05-405c-965c-6fe9b7a36908.dat">
                 <metadata>
-                  <dataset id="7b55dbb89df8f4e5" hid="1"
+                  <dataset id="b842d972534ccb3e" hid="1"
                       size="171.6 KB"
                       edam_format="format_1929"
                       file_ext="fasta" />
-                  <history id="54f2a3a23292eb07"
+                  <history id="8155e4b4bf1581ff"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -42,13 +42,13 @@
     <tracks>
         <track cat="Auto Coloured" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_6.dat" ext="gff3" label="gff3/A.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/7/6/2/dataset_7625da24-6a53-41c2-a7fc-c5c9719deccc.dat" ext="gff3" label="A.gff">
                 <metadata>
-                  <dataset id="fa6d20d0fb68383f" hid="2"
+                  <dataset id="5449172d6ff5669b" hid="2"
                       size="2.3 KB"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="54f2a3a23292eb07"
+                  <history id="8155e4b4bf1581ff"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -66,13 +66,13 @@
                       />
                 </metadata>
               </trackFile>
-              <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_7.dat" ext="gff3" label="gff3/B.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/c/f/c/dataset_cfcde690-dc99-4152-87ef-0936eb90f2ca.dat" ext="gff3" label="B.gff">
                 <metadata>
-                  <dataset id="683bc220e21425bb" hid="3"
+                  <dataset id="9ce08b2254e4d5ed" hid="3"
                       size="2.3 KB"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="54f2a3a23292eb07"
+                  <history id="8155e4b4bf1581ff"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -90,13 +90,13 @@
                       />
                 </metadata>
               </trackFile>
-              <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_8.dat" ext="gff3" label="gff3/C.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/1/c/4/dataset_1c41cecd-9fc6-47b5-9f0b-b7bb73498675.dat" ext="gff3" label="C.gff">
                 <metadata>
-                  <dataset id="a90a30fafe298e1e" hid="4"
+                  <dataset id="80b8022ff3f677b7" hid="4"
                       size="2.3 KB"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="54f2a3a23292eb07"
+                  <history id="8155e4b4bf1581ff"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -114,13 +114,13 @@
                       />
                 </metadata>
               </trackFile>
-              <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_9.dat" ext="gff3" label="gff3/D.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/5/b/3/dataset_5b33c8ff-b12b-4307-a35c-92ea8571dc04.dat" ext="gff3" label="D.gff">
                 <metadata>
-                  <dataset id="b842d972534ccb3e" hid="5"
+                  <dataset id="b54fb481e575bccc" hid="5"
                       size="2.3 KB"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="54f2a3a23292eb07"
+                  <history id="8155e4b4bf1581ff"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -163,20 +163,19 @@
 
                 <gff>
                     <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <topLevelFeatures>mRNA</topLevelFeatures>
                     <index>false</index>
                 </gff>
             </options>
         </track>
         <track cat="Ignore Scale" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
                 <metadata>
-                  <dataset id="5449172d6ff5669b" hid="6"
+                  <dataset id="1ae74d26531588b0" hid="6"
                       size="2.3 KB"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="54f2a3a23292eb07"
+                  <history id="8155e4b4bf1581ff"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -219,20 +218,19 @@
 
                 <gff>
                     <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <topLevelFeatures>mRNA</topLevelFeatures>
                     <index>false</index>
                 </gff>
             </options>
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
                 <metadata>
-                  <dataset id="5449172d6ff5669b" hid="6"
+                  <dataset id="1ae74d26531588b0" hid="6"
                       size="2.3 KB"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="54f2a3a23292eb07"
+                  <history id="8155e4b4bf1581ff"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -281,20 +279,19 @@
 
                 <gff>
                     <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <topLevelFeatures>mRNA</topLevelFeatures>
                     <index>false</index>
                 </gff>
             </options>
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
                 <metadata>
-                  <dataset id="5449172d6ff5669b" hid="6"
+                  <dataset id="1ae74d26531588b0" hid="6"
                       size="2.3 KB"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="54f2a3a23292eb07"
+                  <history id="8155e4b4bf1581ff"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -343,20 +340,19 @@
 
                 <gff>
                     <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <topLevelFeatures>mRNA</topLevelFeatures>
                     <index>false</index>
                 </gff>
             </options>
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
                 <metadata>
-                  <dataset id="5449172d6ff5669b" hid="6"
+                  <dataset id="1ae74d26531588b0" hid="6"
                       size="2.3 KB"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="54f2a3a23292eb07"
+                  <history id="8155e4b4bf1581ff"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -407,20 +403,19 @@
 
                 <gff>
                     <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <topLevelFeatures>mRNA</topLevelFeatures>
                     <index>false</index>
                 </gff>
             </options>
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
                 <metadata>
-                  <dataset id="5449172d6ff5669b" hid="6"
+                  <dataset id="1ae74d26531588b0" hid="6"
                       size="2.3 KB"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="54f2a3a23292eb07"
+                  <history id="8155e4b4bf1581ff"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -471,20 +466,19 @@
 
                 <gff>
                     <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <topLevelFeatures>mRNA</topLevelFeatures>
                     <index>false</index>
                 </gff>
             </options>
         </track>
         <track cat="Realistic" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_11.dat" ext="gff3" label="gff3/interpro.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/0/3/0/dataset_030f551a-fd97-470e-ab58-328d8108783d.dat" ext="gff3" label="interpro.gff">
                 <metadata>
-                  <dataset id="9ce08b2254e4d5ed" hid="7"
+                  <dataset id="440a6c2b5d9efe20" hid="7"
                       size="103.3 KB"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="54f2a3a23292eb07"
+                  <history id="8155e4b4bf1581ff"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -527,20 +521,19 @@
 
                 <gff>
                     <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <topLevelFeatures>mRNA</topLevelFeatures>
                     <index>false</index>
                 </gff>
             </options>
         </track>
         <track cat="Realistic" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_12.dat" ext="gff3" label="gff3/2.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/a/b/b/dataset_abb36b76-2a3a-4353-919e-13c94629303f.dat" ext="gff3" label="2.gff">
                 <metadata>
-                  <dataset id="80b8022ff3f677b7" hid="8"
+                  <dataset id="ea0b941dfbe636f8" hid="8"
                       size="326 bytes"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="54f2a3a23292eb07"
+                  <history id="8155e4b4bf1581ff"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -583,7 +576,6 @@
 
                 <gff>
                     <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <topLevelFeatures>mRNA</topLevelFeatures>
                     <match>cDNA_match</match>
                     <index>false</index>
                 </gff>
diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/menus/test.xml
--- a/test-data/menus/test.xml	Fri Aug 30 03:36:39 2019 -0400
+++ b/test-data/menus/test.xml	Wed Sep 11 09:40:36 2019 -0400
@@ -3,13 +3,13 @@
     <metadata>
         <gencode>11</gencode>
         <genomes>
-              <genome path="/tmp/tmpWtvfKr/files/000/dataset_14.dat">
+              <genome path="/tmp/tmpqkd9zdgq/files/5/7/a/dataset_57af8674-e6c1-464b-9491-a7dade60d738.dat">
                 <metadata>
-                  <dataset id="1ae74d26531588b0" hid="1"
+                  <dataset id="61f03d5eef6f1538" hid="1"
                       size="171.6 KB"
                       edam_format="format_1929"
                       file_ext="fasta" />
-                  <history id="8155e4b4bf1581ff"
+                  <history id="7b55dbb89df8f4e5"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -42,13 +42,13 @@
     <tracks>
         <track cat="With menu or index" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_15.dat" ext="gff3" label="1.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/b/c/d/dataset_bcd9d5b3-9f0f-4350-8628-f282f26cb8d4.dat" ext="gff3" label="1.gff">
                 <metadata>
-                  <dataset id="440a6c2b5d9efe20" hid="2"
+                  <dataset id="d5b3e51b7b790121" hid="2"
                       size="2.3 KB"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="8155e4b4bf1581ff"
+                  <history id="7b55dbb89df8f4e5"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -72,7 +72,7 @@
                 <style>
                     <overridePlugins>False</overridePlugins>
                     <overrideDraggable>False</overrideDraggable>
-                    <className>feature2</className>
+                    <className>feature</className>
                     <description>note,description</description>
                     <label>product,name,id</label>
                     <height>10px</height>
@@ -105,20 +105,19 @@
 
                 <gff>
                     <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <topLevelFeatures>mRNA</topLevelFeatures>
                     <index>false</index>
                 </gff>
             </options>
         </track>
         <track cat="With menu or index" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_15.dat" ext="gff3" label="1.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/b/c/d/dataset_bcd9d5b3-9f0f-4350-8628-f282f26cb8d4.dat" ext="gff3" label="1.gff">
                 <metadata>
-                  <dataset id="440a6c2b5d9efe20" hid="2"
+                  <dataset id="d5b3e51b7b790121" hid="2"
                       size="2.3 KB"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="8155e4b4bf1581ff"
+                  <history id="7b55dbb89df8f4e5"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -142,7 +141,7 @@
                 <style>
                     <overridePlugins>False</overridePlugins>
                     <overrideDraggable>False</overrideDraggable>
-                    <className>feature2</className>
+                    <className>feature</className>
                     <description>note,description</description>
                     <label>product,name,id</label>
                     <height>10px</height>
@@ -161,7 +160,6 @@
 
                 <gff>
                     <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <topLevelFeatures>mRNA</topLevelFeatures>
                     <index>true</index>
                 </gff>
             </options>
diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/track_config/test.xml
--- a/test-data/track_config/test.xml	Fri Aug 30 03:36:39 2019 -0400
+++ b/test-data/track_config/test.xml	Wed Sep 11 09:40:36 2019 -0400
@@ -3,13 +3,13 @@
     <metadata>
         <gencode>11</gencode>
         <genomes>
-              <genome path="/tmp/tmpWtvfKr/files/000/dataset_17.dat">
+              <genome path="/tmp/tmpqkd9zdgq/files/d/0/a/dataset_d0a8a714-9666-4fe5-8083-976a4ba5c6bd.dat">
                 <metadata>
-                  <dataset id="27ee89e2e3d631e0" hid="1"
+                  <dataset id="c18708cec3343c17" hid="1"
                       size="171.6 KB"
                       edam_format="format_1929"
                       file_ext="fasta" />
-                  <history id="7b55dbb89df8f4e5"
+                  <history id="fa6d20d0fb68383f"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -42,13 +42,13 @@
     <tracks>
         <track cat="With canvas config" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_18.dat" ext="gff3" label="1.gff">
+              <trackFile path="/tmp/tmpqkd9zdgq/files/e/5/9/dataset_e597912a-188f-4152-afc7-fd537b2d5a0d.dat" ext="gff3" label="1.gff">
                 <metadata>
-                  <dataset id="61f03d5eef6f1538" hid="2"
+                  <dataset id="5ca39fba41b940d1" hid="2"
                       size="2.3 KB"
                       edam_format="format_1975"
                       file_ext="gff3" />
-                  <history id="7b55dbb89df8f4e5"
+                  <history id="fa6d20d0fb68383f"
                       user_email="test@bx.psu.edu"
                       user_id="2"
                       display_name="test_history"/>
@@ -72,7 +72,7 @@
                 <style>
                     <overridePlugins>False</overridePlugins>
                     <overrideDraggable>False</overrideDraggable>
-                    <className>feature2</className>
+                    <className>feature</className>
                     <description>note,description</description>
                     <label>product,name,id</label>
                     <height>10px</height>