changeset 42:6cd09d7b5f37 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
author iuc
date Sat, 06 Feb 2021 12:01:13 +0000 (2021-02-06)
parents 8774b28235bb
children 4542035c1075
files jbrowse.xml test-data/bam/test.xml test-data/bed/test.xml test-data/custom_config/test.xml test-data/endpoints/test.xml test-data/gencode/test-1.xml test-data/gencode/test-data_table.xml test-data/gencode/test.xml test-data/gff3/test.xml test-data/menus/test.xml test-data/track_config/test.xml
diffstat 11 files changed, 87 insertions(+), 1474 deletions(-) [+]
line wrap: on
line diff
--- a/jbrowse.xml	Thu Dec 31 16:00:42 2020 +0000
+++ b/jbrowse.xml	Sat Feb 06 12:01:13 2021 +0000
@@ -683,7 +683,17 @@
       <param name="gencode" value="1" />
       <param name="standalone" value="data" />
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gencode/test-1.xml" lines_diff="16"/>
+      <output name="output">
+          <assert_contents>
+              <has_text text="&lt;gencode&gt;1&lt;/gencode&gt;"></has_text>
+              <has_text text="genome path="></has_text>
+              <has_text text="dataset id="></has_text>
+              <has_text text="history id="></has_text>
+              <has_text text="metadata"></has_text>
+              <has_text text="tool_id"></has_text>
+
+          </assert_contents>
+      </output>
     </test>
     <test>
       <param name="reference_genome|genome_type_select" value="history"/>
@@ -691,7 +701,16 @@
       <param name="gencode" value="11" />
       <param name="standalone" value="data" />
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gencode/test.xml" lines_diff="16"/>
+      <output name="output">
+        <assert_contents>
+            <has_text text="&lt;gencode&gt;11&lt;/gencode&gt;"></has_text>
+            <has_text text="genome path="></has_text>
+            <has_text text="dataset id="></has_text>
+            <has_text text="history id="></has_text>
+            <has_text text="metadata"></has_text>
+            <has_text text="tool_id"></has_text>
+        </assert_contents>
+    </output>
     </test>
     <test>
       <param name="reference_genome|genome_type_select" value="history"/>
@@ -708,7 +727,19 @@
         </repeat>
       </repeat>
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="bed/test.xml" lines_diff="32"/>
+      <output name="output">
+        <assert_contents>
+            <has_text text="&lt;gencode&gt;11&lt;/gencode&gt;"></has_text>
+            <has_text text="genome path="></has_text>
+            <has_text text="dataset id="></has_text>
+            <has_text text="history id="></has_text>
+            <has_text text="metadata"></has_text>
+            <has_text text="tool_id"></has_text>
+            <has_text text="trackFile path="></has_text>
+            <has_text text="ext=&quot;bed&quot; label=&quot;test-3.bed&quot;"></has_text>
+            <has_text text="NeatHTMLFeatures"></has_text>
+        </assert_contents>
+      </output>
     </test>
     <test>
       <param name="reference_genome|genome_type_select" value="history"/>
@@ -904,7 +935,18 @@
       </repeat>
 
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gff3/test.xml" lines_diff="260" />
+      <output name="output">
+          <assert_contents>
+                <has_text text="Auto Coloured"/>
+                <has_text text="A.gff"/>
+                <has_text text="B.gff"/>
+                <has_text text="C.gff"/>
+                <has_text text="D.gff"/>
+                <has_text text="Scaled Colour"/>
+                <has_text text="1.gff"/>
+                <has_text text="2.gff"/>
+          </assert_contents>
+      </output>
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -967,7 +1009,14 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="menus/test.xml" lines_diff="44"/>
+        <output name="output">
+            <assert_contents>
+                <has_text text="With menu or index"/>
+                <has_text text="Some menu item"/>
+                <has_text text="Frame title"/>
+                <has_text text="dijitIconNewTask"/>
+            </assert_contents>
+        </output>
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -1005,7 +1054,13 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="track_config/test.xml" lines_diff="30"/>
+        <output name="output">
+            <assert_contents>
+                <has_text text="With canvas config"></has_text>
+                <has_text text="&lt;transcriptType&gt;transcript&lt;/transcriptType&gt;"></has_text>
+                <has_text text="&lt;subParts&gt;exon&lt;/subParts&gt;"></has_text>
+            </assert_contents>
+        </output>
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -1057,7 +1112,15 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="custom_config/test.xml" lines_diff="30"/>
+        <output name="output">
+            <assert_contents>
+                <has_text text="1.gff"/>
+                <has_text text="collapsed"/>
+                <has_text text="150"/>
+                <has_text text="maxFeatureScreenDensity"/>
+                <has_text text="style.strandArrow"/>
+            </assert_contents>
+        </output>
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -1076,7 +1139,13 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="bam/test.xml" lines_diff="42"/>
+        <output name="output">
+            <assert_contents>
+                <has_text text="merlin-sample.bam"/>
+                <has_text text="sort_order=&quot;coordinate&quot;"/>
+                <has_text text="bam_index"/>
+            </assert_contents>
+        </output>
     </test>
 
     <test>
@@ -1086,7 +1155,11 @@
         <param name="gencode" value="1" />
         <param name="standalone" value="data" />
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
+        <output name="output">
+            <assert_contents>
+                <has_text text="merlin.fa"/>
+            </assert_contents>
+        </output>
     </test>
 
     <test>
@@ -1133,7 +1206,11 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="endpoints/test.xml" lines_diff="16"/>
+        <output name="output">
+            <assert_contents>
+                <has_text text="http://example.org.external/sparql/"/>
+            </assert_contents>
+        </output>
     </test>
   </tests>
   <help><![CDATA[
--- a/test-data/bam/test.xml	Thu Dec 31 16:00:42 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-<?xml version="1.0"?>
-<root>
-    <metadata>
-        <gencode>11</gencode>
-        <genomes>
-              <genome path="/tmp/tmpqkd9zdgq/files/d/3/d/dataset_d3d20b83-6a77-4e76-bb7e-3b9fe7261453.dat">
-                <metadata>
-                  <dataset id="238993350abc9bfd" hid="1"
-                      size="171.6 KB"
-                      edam_format="format_1929"
-                      file_ext="fasta" />
-                  <history id="a90a30fafe298e1e"
-                      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="Auto Coloured" format="pileup" visibility="default_off">
-            <files>
-              <trackFile path="/tmp/tmpqkd9zdgq/files/6/a/0/dataset_6a00d93a-ee34-42d5-897b-9470d6c71e1f.dat" ext="bam" label="merlin-sample.bam">
-                <metadata>
-                  <dataset id="adba32ec9811aba7" hid="2"
-                      size="12.9 KB"
-                      edam_format="format_2572"
-                      file_ext="bam" />
-                  <history id="a90a30fafe298e1e"
-                      user_email="test@bx.psu.edu"
-                      user_id="2"
-                      display_name="test_history"/>
-                  <metadata
-                      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 7f3deb10ba10 on: u__sq__Merlin__sq__]"
-                      reference_lengths="[172788]"
-                      columns="12"
-                      bam_index="__lt__galaxy.model.MetadataFile(1) at 0x7f3de95da7d0__gt__"
-                      />
-                  <tool
-                      tool_id="upload1"
-                      tool_version="1.1.6"
-                      />
-                </metadata>
-              </trackFile>
-            </files>
-
-            <options>
-                <custom_config>
-                </custom_config>
-
-                <pileup>
-                    <auto_snp>false</auto_snp>
-                    <bam_indices>
-                        <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>
-            </options>
-        </track>
-    </tracks>
-    <plugins
-        ComboTrackSelector=""
-        Bookmarks=""
-        GCContent=""
-        BlastView="True"
-        theme=""
-        />
-</root>
--- a/test-data/bed/test.xml	Thu Dec 31 16:00:42 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,136 +0,0 @@
-<?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>
--- a/test-data/custom_config/test.xml	Thu Dec 31 16:00:42 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,118 +0,0 @@
-<?xml version="1.0"?>
-<root>
-    <metadata>
-        <gencode>11</gencode>
-        <genomes>
-              <genome path="/tmp/tmpqkd9zdgq/files/1/a/7/dataset_1a77d084-9f64-48b9-802b-787e0e86c7b1.dat">
-                <metadata>
-                  <dataset id="a1e670e1ea0da54b" hid="1"
-                      size="171.6 KB"
-                      edam_format="format_1929"
-                      file_ext="fasta" />
-                  <history id="683bc220e21425bb"
-                      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="With custom track config" format="gene_calls" visibility="default_off">
-            <files>
-              <trackFile path="/tmp/tmpqkd9zdgq/files/a/4/a/dataset_a4a9adc4-f3d3-4c05-8074-69e01ace1c78.dat" ext="gff3" label="1.gff">
-                <metadata>
-                  <dataset id="9a22496ee796fbfc" hid="2"
-                      size="2.3 KB"
-                      edam_format="format_1975"
-                      file_ext="gff3" />
-                  <history id="683bc220e21425bb"
-                      user_email="test@bx.psu.edu"
-                      user_id="2"
-                      display_name="test_history"/>
-                  <metadata
-                      dbkey="?"
-                      data_lines="27"
-                      comment_lines="19"
-                      columns="9"
-                      delimiter="__tc__"
-                      attributes="6"
-                      />
-                  <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>
-                  <displayMode>
-                    <text>collapsed</text>
-                  </displayMode>
-                  <histograms.height>
-                    <integer>150</integer>
-                  </histograms.height>
-                  <maxFeatureScreenDensity>
-                    <float>0.1</float>
-                  </maxFeatureScreenDensity>
-                  <style.strandArrow>
-                    <boolean>false</boolean>
-                  </style.strandArrow>
-                </custom_config>
-
-                <gff>
-                    <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <index>false</index>
-                </gff>
-            </options>
-        </track>
-    </tracks>
-    <plugins
-        ComboTrackSelector=""
-        Bookmarks=""
-        GCContent=""
-        BlastView="True"
-        theme=""
-        />
-</root>
--- a/test-data/endpoints/test.xml	Thu Dec 31 16:00:42 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,106 +0,0 @@
-<?xml version="1.0"?>
-<root>
-    <metadata>
-        <gencode>11</gencode>
-        <genomes>
-              <genome path="/tmp/tmpqkd9zdgq/files/9/5/5/dataset_955a2615-e4c3-4ccc-ae7b-749a589abc12.dat">
-                <metadata>
-                  <dataset id="27a22803849b1486" hid="1"
-                      size="171.6 KB"
-                      edam_format="format_1929"
-                      file_ext="fasta" />
-                  <history id="5449172d6ff5669b"
-                      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="External endpoints" format="rest" visibility="default_off">
-
-            <options>
-                <style>
-                    <overridePlugins>False</overridePlugins>
-                    <overrideDraggable>False</overrideDraggable>
-                    <className>feature</className>
-                    <description>Hit_titles</description>
-                    <label>description</label>
-                    <height>600px</height>
-                    <maxHeight>600</maxHeight>
-                </style>
-                <scaling>
-                        <method>ignore</method>
-                        <scheme>
-                            <color>__auto__</color>
-                        </scheme>
-                </scaling>
-                <menus>
-                </menus>
-
-                <label>Rest api</label>
-                <rest>
-                    <url>http://example.org.external/rest_api/</url>
-                </rest>
-            </options>
-        </track>
-        <track cat="External endpoints" format="sparql" visibility="default_off">
-
-            <options>
-                <style>
-                    <overridePlugins>False</overridePlugins>
-                    <overrideDraggable>False</overrideDraggable>
-                    <className>feature</className>
-                    <description>Hit_titles</description>
-                    <label>description</label>
-                    <height>600px</height>
-                    <maxHeight>600</maxHeight>
-                </style>
-                <scaling>
-                        <method>ignore</method>
-                        <scheme>
-                            <color>__auto__</color>
-                        </scheme>
-                </scaling>
-                <menus>
-                </menus>
-
-                <label>Sparql endpoint</label>
-                <sparql>
-                    <url>http://example.org.external/sparql/</url>
-                    <query>  DEFINE sql:select-option 'order'   prefix rdf:    __lt__http://www.w3.org/1999/02/22-rdf-syntax-ns#__gt__   select ?start,          ?end,          IF( ?faldo_type = faldo:ForwardStrandPosition,              1,              IF( ?faldo_type = faldo:ReverseStrandPosition,                  -1,                   0                )            ) as ?strand,          str(?obj_type_name) as ?type,          str(?label) as ?name,          str(?obj_name) as ?description,          ?obj as ?uniqueID,          ?parent as ?parentUniqueID   where {     values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition }   }</query>
-                </sparql>
-            </options>
-        </track>
-    </tracks>
-    <plugins
-        ComboTrackSelector=""
-        Bookmarks=""
-        GCContent=""
-        BlastView="True"
-        theme=""
-        />
-</root>
--- a/test-data/gencode/test-1.xml	Thu Dec 31 16:00:42 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-<?xml version="1.0"?>
-<root>
-    <metadata>
-        <gencode>1</gencode>
-        <genomes>
-              <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"
-                      edam_format="format_1929"
-                      file_ext="fasta" />
-                  <history id="2891970512fa2d5a"
-                      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>
-    </tracks>
-    <plugins
-        ComboTrackSelector=""
-        Bookmarks=""
-        GCContent=""
-        BlastView="True"
-        theme=""
-        />
-</root>
--- a/test-data/gencode/test-data_table.xml	Thu Dec 31 16:00:42 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-<?xml version="1.0"?>
-<root>
-    <metadata>
-        <gencode>1</gencode>
-        <genomes>
-              <genome path="/home/hxr/arbeit/tools-iuc/tools/jbrowse/test-data/merlin.fa">
-                  <metadata />
-              </genome>s
-        </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>
-    </tracks>
-    <plugins
-        ComboTrackSelector=""
-        Bookmarks=""
-        GCContent=""
-        BlastView="True"
-        theme=""
-        />
-</root>
--- a/test-data/gencode/test.xml	Thu Dec 31 16:00:42 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-<?xml version="1.0"?>
-<root>
-    <metadata>
-        <gencode>11</gencode>
-        <genomes>
-              <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"
-                      edam_format="format_1929"
-                      file_ext="fasta" />
-                  <history id="5729865256bc2525"
-                      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>
-    </tracks>
-    <plugins
-        ComboTrackSelector=""
-        Bookmarks=""
-        GCContent=""
-        BlastView="True"
-        theme=""
-        />
-</root>
--- a/test-data/gff3/test.xml	Thu Dec 31 16:00:42 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,592 +0,0 @@
-<?xml version="1.0"?>
-<root>
-    <metadata>
-        <gencode>11</gencode>
-        <genomes>
-              <genome path="/tmp/tmpqkd9zdgq/files/b/f/a/dataset_bfad32fe-cc05-405c-965c-6fe9b7a36908.dat">
-                <metadata>
-                  <dataset id="b842d972534ccb3e" hid="1"
-                      size="171.6 KB"
-                      edam_format="format_1929"
-                      file_ext="fasta" />
-                  <history id="8155e4b4bf1581ff"
-                      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="Auto Coloured" format="gene_calls" visibility="default_off">
-            <files>
-              <trackFile path="/tmp/tmpqkd9zdgq/files/7/6/2/dataset_7625da24-6a53-41c2-a7fc-c5c9719deccc.dat" ext="gff3" label="A.gff">
-                <metadata>
-                  <dataset id="5449172d6ff5669b" hid="2"
-                      size="2.3 KB"
-                      edam_format="format_1975"
-                      file_ext="gff3" />
-                  <history id="8155e4b4bf1581ff"
-                      user_email="test@bx.psu.edu"
-                      user_id="2"
-                      display_name="test_history"/>
-                  <metadata
-                      dbkey="?"
-                      data_lines="27"
-                      comment_lines="19"
-                      columns="9"
-                      delimiter="__tc__"
-                      attributes="6"
-                      />
-                  <tool
-                      tool_id="upload1"
-                      tool_version="1.1.6"
-                      />
-                </metadata>
-              </trackFile>
-              <trackFile path="/tmp/tmpqkd9zdgq/files/c/f/c/dataset_cfcde690-dc99-4152-87ef-0936eb90f2ca.dat" ext="gff3" label="B.gff">
-                <metadata>
-                  <dataset id="9ce08b2254e4d5ed" hid="3"
-                      size="2.3 KB"
-                      edam_format="format_1975"
-                      file_ext="gff3" />
-                  <history id="8155e4b4bf1581ff"
-                      user_email="test@bx.psu.edu"
-                      user_id="2"
-                      display_name="test_history"/>
-                  <metadata
-                      dbkey="?"
-                      data_lines="27"
-                      comment_lines="19"
-                      columns="9"
-                      delimiter="__tc__"
-                      attributes="6"
-                      />
-                  <tool
-                      tool_id="upload1"
-                      tool_version="1.1.6"
-                      />
-                </metadata>
-              </trackFile>
-              <trackFile path="/tmp/tmpqkd9zdgq/files/1/c/4/dataset_1c41cecd-9fc6-47b5-9f0b-b7bb73498675.dat" ext="gff3" label="C.gff">
-                <metadata>
-                  <dataset id="80b8022ff3f677b7" hid="4"
-                      size="2.3 KB"
-                      edam_format="format_1975"
-                      file_ext="gff3" />
-                  <history id="8155e4b4bf1581ff"
-                      user_email="test@bx.psu.edu"
-                      user_id="2"
-                      display_name="test_history"/>
-                  <metadata
-                      dbkey="?"
-                      data_lines="27"
-                      comment_lines="19"
-                      columns="9"
-                      delimiter="__tc__"
-                      attributes="6"
-                      />
-                  <tool
-                      tool_id="upload1"
-                      tool_version="1.1.6"
-                      />
-                </metadata>
-              </trackFile>
-              <trackFile path="/tmp/tmpqkd9zdgq/files/5/b/3/dataset_5b33c8ff-b12b-4307-a35c-92ea8571dc04.dat" ext="gff3" label="D.gff">
-                <metadata>
-                  <dataset id="b54fb481e575bccc" hid="5"
-                      size="2.3 KB"
-                      edam_format="format_1975"
-                      file_ext="gff3" />
-                  <history id="8155e4b4bf1581ff"
-                      user_email="test@bx.psu.edu"
-                      user_id="2"
-                      display_name="test_history"/>
-                  <metadata
-                      dbkey="?"
-                      data_lines="27"
-                      comment_lines="19"
-                      columns="9"
-                      delimiter="__tc__"
-                      attributes="6"
-                      />
-                  <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>
-        <track cat="Ignore Scale" format="gene_calls" visibility="default_off">
-            <files>
-              <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
-                <metadata>
-                  <dataset id="1ae74d26531588b0" hid="6"
-                      size="2.3 KB"
-                      edam_format="format_1975"
-                      file_ext="gff3" />
-                  <history id="8155e4b4bf1581ff"
-                      user_email="test@bx.psu.edu"
-                      user_id="2"
-                      display_name="test_history"/>
-                  <metadata
-                      dbkey="?"
-                      data_lines="27"
-                      comment_lines="19"
-                      columns="9"
-                      delimiter="__tc__"
-                      attributes="6"
-                      />
-                  <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>#ff00ff</color>
-                        </scheme>
-                </scaling>
-                <menus>
-                </menus>
-                <custom_config>
-                </custom_config>
-
-                <gff>
-                    <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <index>false</index>
-                </gff>
-            </options>
-        </track>
-        <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
-            <files>
-              <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
-                <metadata>
-                  <dataset id="1ae74d26531588b0" hid="6"
-                      size="2.3 KB"
-                      edam_format="format_1975"
-                      file_ext="gff3" />
-                  <history id="8155e4b4bf1581ff"
-                      user_email="test@bx.psu.edu"
-                      user_id="2"
-                      display_name="test_history"/>
-                  <metadata
-                      dbkey="?"
-                      data_lines="27"
-                      comment_lines="19"
-                      columns="9"
-                      delimiter="__tc__"
-                      attributes="6"
-                      />
-                  <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>score</method>
-                        <algo>linear</algo>
-                        <scales>
-                            <type>automatic</type>
-
-                        </scales>
-                        <scheme>
-                            <type>opacity</type>
-                            <color>__auto__</color>
-                        </scheme>
-                </scaling>
-                <menus>
-                </menus>
-                <custom_config>
-                </custom_config>
-
-                <gff>
-                    <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <index>false</index>
-                </gff>
-            </options>
-        </track>
-        <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
-            <files>
-              <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
-                <metadata>
-                  <dataset id="1ae74d26531588b0" hid="6"
-                      size="2.3 KB"
-                      edam_format="format_1975"
-                      file_ext="gff3" />
-                  <history id="8155e4b4bf1581ff"
-                      user_email="test@bx.psu.edu"
-                      user_id="2"
-                      display_name="test_history"/>
-                  <metadata
-                      dbkey="?"
-                      data_lines="27"
-                      comment_lines="19"
-                      columns="9"
-                      delimiter="__tc__"
-                      attributes="6"
-                      />
-                  <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>score</method>
-                        <algo>linear</algo>
-                        <scales>
-                            <type>automatic</type>
-
-                        </scales>
-                        <scheme>
-                            <type>opacity</type>
-                            <color>#0000ff</color>
-                        </scheme>
-                </scaling>
-                <menus>
-                </menus>
-                <custom_config>
-                </custom_config>
-
-                <gff>
-                    <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <index>false</index>
-                </gff>
-            </options>
-        </track>
-        <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
-            <files>
-              <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
-                <metadata>
-                  <dataset id="1ae74d26531588b0" hid="6"
-                      size="2.3 KB"
-                      edam_format="format_1975"
-                      file_ext="gff3" />
-                  <history id="8155e4b4bf1581ff"
-                      user_email="test@bx.psu.edu"
-                      user_id="2"
-                      display_name="test_history"/>
-                  <metadata
-                      dbkey="?"
-                      data_lines="27"
-                      comment_lines="19"
-                      columns="9"
-                      delimiter="__tc__"
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-                  <tool
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-                      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>score</method>
-                        <algo>linear</algo>
-                        <scales>
-                            <type>manual</type>
-
-                            <min>0</min>
-                            <max>1000</max>
-                        </scales>
-                        <scheme>
-                            <type>opacity</type>
-                            <color>__auto__</color>
-                        </scheme>
-                </scaling>
-                <menus>
-                </menus>
-                <custom_config>
-                </custom_config>
-
-                <gff>
-                    <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <index>false</index>
-                </gff>
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-        </track>
-        <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
-            <files>
-              <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">
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-                  <history id="8155e4b4bf1581ff"
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-                  <tool
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-            <options>
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-                    <label>product,name,id</label>
-                    <height>10px</height>
-                    <maxHeight>600</maxHeight>
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-                <scaling>
-                        <method>score</method>
-                        <algo>linear</algo>
-                        <scales>
-                            <type>manual</type>
-
-                            <min>0</min>
-                            <max>1000</max>
-                        </scales>
-                        <scheme>
-                            <type>opacity</type>
-                            <color>#ff0000</color>
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-                <custom_config>
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-                <gff>
-                    <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
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-            <options>
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-                    <maxHeight>600</maxHeight>
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-                <gff>
-                    <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
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-            </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>
-                    <match>cDNA_match</match>
-                    <index>false</index>
-                </gff>
-            </options>
-        </track>
-    </tracks>
-    <plugins
-        ComboTrackSelector=""
-        Bookmarks=""
-        GCContent=""
-        BlastView="True"
-        theme=""
-        />
-</root>
--- a/test-data/menus/test.xml	Thu Dec 31 16:00:42 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,175 +0,0 @@
-<?xml version="1.0"?>
-<root>
-    <metadata>
-        <gencode>11</gencode>
-        <genomes>
-              <genome path="/tmp/tmpqkd9zdgq/files/5/7/a/dataset_57af8674-e6c1-464b-9491-a7dade60d738.dat">
-                <metadata>
-                  <dataset id="61f03d5eef6f1538" hid="1"
-                      size="171.6 KB"
-                      edam_format="format_1929"
-                      file_ext="fasta" />
-                  <history id="7b55dbb89df8f4e5"
-                      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="With menu or index" format="gene_calls" visibility="default_off">
-            <files>
-              <trackFile path="/tmp/tmpqkd9zdgq/files/b/c/d/dataset_bcd9d5b3-9f0f-4350-8628-f282f26cb8d4.dat" ext="gff3" label="1.gff">
-                <metadata>
-                  <dataset id="d5b3e51b7b790121" hid="2"
-                      size="2.3 KB"
-                      edam_format="format_1975"
-                      file_ext="gff3" />
-                  <history id="7b55dbb89df8f4e5"
-                      user_email="test@bx.psu.edu"
-                      user_id="2"
-                      display_name="test_history"/>
-                  <metadata
-                      dbkey="?"
-                      data_lines="27"
-                      comment_lines="19"
-                      columns="9"
-                      delimiter="__tc__"
-                      attributes="6"
-                      />
-                  <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>
-                  <menu>
-                    <action>iframeDialog</action>
-                      <label>Some menu item</label>
-                      <title>Frame title</title>
-                      <url>https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;</url>
-                      <iconClass>dijitIconNewTask</iconClass>
-                  </menu>
-                  <menu>
-                    <action>newWindow</action>
-                      <label>Another menu item</label>
-                      <title>Frame title 2</title>
-                      <url>https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;</url>
-                      <iconClass>dijitIconBookmark</iconClass>
-                  </menu>
-                </menus>
-                <custom_config>
-                </custom_config>
-
-                <gff>
-                    <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
-                    <index>false</index>
-                </gff>
-            </options>
-        </track>
-        <track cat="With menu or index" format="gene_calls" visibility="default_off">
-            <files>
-              <trackFile path="/tmp/tmpqkd9zdgq/files/b/c/d/dataset_bcd9d5b3-9f0f-4350-8628-f282f26cb8d4.dat" ext="gff3" label="1.gff">
-                <metadata>
-                  <dataset id="d5b3e51b7b790121" hid="2"
-                      size="2.3 KB"
-                      edam_format="format_1975"
-                      file_ext="gff3" />
-                  <history id="7b55dbb89df8f4e5"
-                      user_email="test@bx.psu.edu"
-                      user_id="2"
-                      display_name="test_history"/>
-                  <metadata
-                      dbkey="?"
-                      data_lines="27"
-                      comment_lines="19"
-                      columns="9"
-                      delimiter="__tc__"
-                      attributes="6"
-                      />
-                  <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>true</index>
-                </gff>
-            </options>
-        </track>
-    </tracks>
-    <plugins
-        ComboTrackSelector=""
-        Bookmarks=""
-        GCContent=""
-        BlastView="True"
-        theme=""
-        />
-</root>
--- a/test-data/track_config/test.xml	Thu Dec 31 16:00:42 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,109 +0,0 @@
-<?xml version="1.0"?>
-<root>
-    <metadata>
-        <gencode>11</gencode>
-        <genomes>
-              <genome path="/tmp/tmpqkd9zdgq/files/d/0/a/dataset_d0a8a714-9666-4fe5-8083-976a4ba5c6bd.dat">
-                <metadata>
-                  <dataset id="c18708cec3343c17" hid="1"
-                      size="171.6 KB"
-                      edam_format="format_1929"
-                      file_ext="fasta" />
-                  <history id="fa6d20d0fb68383f"
-                      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="With canvas config" format="gene_calls" visibility="default_off">
-            <files>
-              <trackFile path="/tmp/tmpqkd9zdgq/files/e/5/9/dataset_e597912a-188f-4152-afc7-fd537b2d5a0d.dat" ext="gff3" label="1.gff">
-                <metadata>
-                  <dataset id="5ca39fba41b940d1" hid="2"
-                      size="2.3 KB"
-                      edam_format="format_1975"
-                      file_ext="gff3" />
-                  <history id="fa6d20d0fb68383f"
-                      user_email="test@bx.psu.edu"
-                      user_id="2"
-                      display_name="test_history"/>
-                  <metadata
-                      dbkey="?"
-                      data_lines="27"
-                      comment_lines="19"
-                      columns="9"
-                      delimiter="__tc__"
-                      attributes="6"
-                      />
-                  <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>JBrowse/View/Track/CanvasFeatures</trackType>
-                    <transcriptType>transcript</transcriptType>
-                    <subParts>exon</subParts>
-                    <impliedUTRs>true</impliedUTRs>
-                    <index>false</index>
-                </gff>
-            </options>
-        </track>
-    </tracks>
-    <plugins
-        ComboTrackSelector=""
-        Bookmarks=""
-        GCContent=""
-        BlastView="True"
-        theme=""
-        />
-</root>