# HG changeset patch
# User iuc
# Date 1761292240 0
# Node ID e237edee9a5398c4b74b863896d0377197ab2aa4
# Parent  93fdd696c281b71bfad5e2e2aed0d01fe52b98e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse2 commit 5482aa86f906615d9bddcc32cfbc2d45b24e6345

diff -r 93fdd696c281 -r e237edee9a53 jbrowse2.py
--- a/jbrowse2.py	Thu Oct 02 10:20:29 2025 +0000
+++ b/jbrowse2.py	Fri Oct 24 07:50:40 2025 +0000
@@ -31,7 +31,9 @@
     "}": "__cc__",
     "@": "__at__",
     "#": "__pd__",
-    "": "__cn__",
+    "\n": "__cn__",
+    "\r": "__cr__",
+    "\t": "__tc__",
 }
 
 
@@ -62,6 +64,14 @@
 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
 
 
+def unsanitize(input):
+
+    for key, value in mapped_chars.items():
+        input = input.replace(value, key)
+
+    return input
+
+
 def metadata_from_node(node):
     metadata = {}
 
@@ -74,7 +84,7 @@
             metadata[f"history_{key}"] = value
 
         for key, value in node.findall("metadata")[0].attrib.items():
-            metadata[f"metadata_{key}"] = value
+            metadata[f"metadata_{key}"] = unsanitize(value)
 
         for key, value in node.findall("tool")[0].attrib.items():
             metadata[f"tool_{key}"] = value
@@ -265,15 +275,11 @@
         }
 
         if "feature" in xml_conf["formatdetails"]:
-            feat_jexl = xml_conf["formatdetails"]["feature"]
-            for key, value in mapped_chars.items():
-                feat_jexl = feat_jexl.replace(value, key)
+            feat_jexl = unsanitize(xml_conf["formatdetails"]["feature"])
             formatDetails["feature"] = feat_jexl
 
         if "subfeature" in xml_conf["formatdetails"]:
-            sfeat_jexl = xml_conf["formatdetails"]["subfeature"]
-            for key, value in mapped_chars.items():
-                sfeat_jexl = sfeat_jexl.replace(value, key)
+            sfeat_jexl = unsanitize(xml_conf["formatdetails"]["subfeature"])
             formatDetails["subfeatures"] = sfeat_jexl
 
         if "depth" in xml_conf["formatdetails"]:
@@ -773,6 +779,54 @@
             remote=trackData['remote']
         )
 
+    def add_gtf(self, parent, data, format, trackData, gffOpts, **kwargs):
+        # Not a super recommended format
+        # https://github.com/GMOD/jbrowse-components/pull/2389
+        # https://github.com/GMOD/jbrowse-components/issues/3876
+        if trackData['remote']:
+            rel_dest = data
+        else:
+            rel_dest = os.path.join("data", trackData["label"] + ".gtf")
+            dest = os.path.join(self.outdir, rel_dest)
+            shutil.copy(os.path.realpath(data), dest)
+
+        json_track_data = {
+            "type": "FeatureTrack",
+            "trackId": trackData["label"],
+            "name": trackData["key"],
+            "adapter": {
+                "type": "GtfAdapter",
+                "gtfLocation": {
+                    "uri": rel_dest,
+                    "locationType": "UriLocation"
+                },
+            },
+            "category": [trackData["category"]],
+            "assemblyNames": [parent['uniq_id']],
+        }
+
+        style_json = self._prepare_track_style(trackData)
+
+        formatdetails = self._prepare_format_details(trackData)
+
+        style_json.update(formatdetails)
+
+        track_metadata = self._prepare_track_metadata(trackData)
+
+        style_json.update(track_metadata)
+
+        json_track_data.update(style_json)
+
+        self.subprocess_check_call(
+            [
+                "jbrowse",
+                "add-track-json",
+                "--target",
+                self.outdir,
+                json.dumps(json_track_data),
+            ]
+        )
+
     def add_bed(self, parent, data, format, trackData, gffOpts, **kwargs):
         if trackData['remote']:
             rel_dest = data
@@ -1115,8 +1169,7 @@
             extra_metadata,
         ) in enumerate(track["trackfiles"]):
             # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
-            for key, value in mapped_chars.items():
-                track_human_label = track_human_label.replace(value, key)
+            track_human_label = unsanitize(track_human_label)
 
             is_multi = type(dataset_path) is list
 
@@ -1180,6 +1233,14 @@
                     outputTrackConfig,
                     track["conf"]["options"]["gff"],
                 )
+            elif dataset_ext in ("gtf"):
+                self.add_gtf(
+                    parent,
+                    dataset_path,
+                    dataset_ext,
+                    outputTrackConfig,
+                    track["conf"]["options"]["gff"],
+                )
             elif dataset_ext == "bed":
                 self.add_bed(
                     parent,
@@ -1288,13 +1349,10 @@
                     track["conf"]["options"]["hic"]
                 )
             elif dataset_ext == "sparql":
-                sparql_query = track["conf"]["options"]["sparql"]["query"]
-                for key, value in mapped_chars.items():
-                    sparql_query = sparql_query.replace(value, key)
+                sparql_query = unsanitize(track["conf"]["options"]["sparql"]["query"])
                 sparql_query_refnames = track["conf"]["options"]["sparql"].get("query_refnames", "")
                 if sparql_query_refnames:
-                    for key, value in mapped_chars.items():
-                        sparql_query_refnames = sparql_query_refnames.replace(value, key)
+                    sparql_query_refnames = unsanitize(sparql_query_refnames)
                 self.add_sparql(
                     parent,
                     track["conf"]["options"]["sparql"]["url"],
@@ -1308,7 +1366,7 @@
                     outputTrackConfig,
                 )
             else:
-                log.error(f"Do not know how to handle {dataset_ext}")
+                raise RuntimeError(f"Do not know how to handle dataset of type '{dataset_ext}'")
 
             track_labels.append(outputTrackConfig["label"])
 
@@ -1710,7 +1768,8 @@
 
             track_labels = jc.process_annotations(track_conf, genome)
 
-            if track.attrib["visibility"] == "default_on":
+            if track.attrib["visibility"] == "default_on" and \
+               (track_conf["format"] != "synteny" or track_conf["style"]["display"] != "LinearSyntenyDisplay"):
                 for tlabel in track_labels:
                     default_tracks_on.append(tlabel)
 
diff -r 93fdd696c281 -r e237edee9a53 jbrowse2.xml
--- a/jbrowse2.xml	Thu Oct 02 10:20:29 2025 +0000
+++ b/jbrowse2.xml	Fri Oct 24 07:50:40 2025 +0000
@@ -85,7 +85,7 @@
                     display_name="Unnamed History"/>
                     #end if
                 <metadata
-                    #for (key, value) in $assembly.reference_genome.genome.get_metadata().items():
+                    #for (key, value) in $assembly.reference_genome.genome.metadata.items():
                     #if "_types" not in $key:
                     #if isinstance($value, list):
                         #set value_str = "[%s]" % ','.join([str(val) for val in value])
@@ -144,8 +144,12 @@
                             display_name="Unnamed History"/>
                             #end if
                         <metadata
-                            #for (key, value) in $dataset.get_metadata().items():
-                            #if "_types" not in $key and $value is not None and len(str($value)) < 5000:
+                            #for (key, value) in $dataset.metadata.items():
+                            ## Skip a few useless metadata
+                            ##   _index = internal paths to index files
+                            ##   species_chromosomes = internal path to .len file
+                            ##   metadata_incomplete = internal galaxy stuff
+                            #if "_types" not in $key and not $key.endswith("_index") and $key != "species_chromosomes" and $key != "metadata_incomplete" and $value is not None and len(str($value)) < 5000:
                             #if isinstance($value, list) or isinstance($value, dict):
                                 #set value_str = json.dumps(value).replace('"', "&quot;")
                                 ${key}="${value_str}"
@@ -310,7 +314,7 @@
             </when>
         </conditional>
 
-        <repeat name="assemblies" min="1" title="Genome Assemblies">
+        <repeat name="assemblies" min="1" title="Genome Assembly">
         <conditional name="reference_genome">
             <param label="Reference genome to display" name="genome_type_select" type="select">
                 <option selected="True" value="indexed">Use a built-in genome</option>
@@ -348,19 +352,21 @@
              https://github.com/GMOD/jbrowse-components/issues/1765
         -->
 
-        <param label="Default region to display" type="text" name="defaultLocation" value="" help="e.g. 'ctgA:1234..5678'"/>
+        <param label="Default region to display" type="text" name="defaultLocation" value="" help="e.g. 'ctgA:1234..5678'">
+            <validator type="expression" message="Region should be like ctgA:1234..5678">'^[a-zA-Z0-9_]:\d+\.\.\d+$'</validator>
+        </param>
 
         <param name="ref_name_aliases" type="data" format="tsv,tabular" label="Reference sequence name aliases" help="Use when chromosomes have alternate names (TSV file: first column is the names from your genome sequence, the rest of the columns are aliases." optional="true" />
 
         <param name="cytobands" type="data" format="bed" label="cytobands data" help="BED file containing cytobands locations" optional="true" />
 
-        <repeat name="track_groups" title="Track Group">
-            <param label="Track Category"
+        <repeat name="track_groups" title="Track Category" help="Organise your tracks into different Categories for a nicer end-user experience.">
+            <param label="Track Category Label"
                 name="category"
                 type="text"
                 value="Default"
-                help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
-            <repeat name="data_tracks" title="Annotation Track">
+                help="You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
+            <repeat name="data_tracks" title="Track">
                 <conditional name="data_format" label="Track Options">
                     <param type="select" label="Track Type" name="data_format_select">
                         <option value="gene_calls">GFF/GFF3/BED Features</option>
@@ -375,7 +381,7 @@
                         <option value="gc">GC content</option>
                     </param>
                     <when value="gene_calls">
-                        <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
+                        <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" help="GTF format is supported but GFF should be preferred" />
 
                         <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
 
@@ -512,6 +518,15 @@
                     </repeat>
                     <repeat name="data_tracks">
                         <conditional name="data_format">
+                            <param name="data_format_select" value="gene_calls" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="gtf/merlin.gtf" ftype="gtf" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
                             <param name="data_format_select" value="gene_calls"/>
                             <conditional name="annotation_cond">
                                 <param name="annotation_source" value="history" />
@@ -593,8 +608,12 @@
                 </repeat>
             </repeat>
             <output name="output">
-                <extra_files name="galaxy.xml" type="file" value="out/01_all_tracks/galaxy.xml" compare="sim_size" />
-                <extra_files name="config.json" type="file" value="out/01_all_tracks/config.json" compare="sim_size" />
+                <extra_files name="galaxy.xml" type="file" value="out/01_all_tracks/galaxy.xml" compare="sim_size" delta="0">
+                    <assert_contents>
+                        <is_valid_xml />
+                    </assert_contents>
+                </extra_files>
+                <extra_files name="config.json" type="file" value="out/01_all_tracks/config.json" compare="sim_size" delta="0" />
             </output>
         </test>
         <test> <!-- Remote data -->
@@ -703,8 +722,17 @@
                 </repeat>
             </repeat>
             <output name="output">
-                <extra_files name="galaxy.xml" type="file" value="out/02_remote/galaxy.xml" compare="sim_size" />
-                <extra_files name="config.json" type="file" value="out/02_remote/config.json" compare="sim_size" />
+                <extra_files name="galaxy.xml" type="file" value="out/02_remote/galaxy.xml" compare="sim_size" delta="0">
+                    <assert_contents>
+                        <is_valid_xml />
+                    </assert_contents>
+                </extra_files>
+                <extra_files name="config.json" type="file" value="out/02_remote/config.json" compare="sim_size" delta="0">
+                    <assert_contents>
+                        <has_json_property_with_value property="adapter" value="{&quot;type&quot;:&quot;BigWigAdapter&quot;,&quot;bigWigLocation&quot;:{&quot;uri&quot;:&quot;https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw&quot;,&quot;locationType&quot;:&quot;UriLocation&quot;}}" />
+                        <has_json_property_with_value property="adapter" value="{&quot;type&quot;:&quot;MultiWiggleAdapter&quot;,&quot;subadapters&quot;:[{&quot;type&quot;:&quot;BigWigAdapter&quot;,&quot;name&quot;:&quot;SKBR3 pacbio coverage (NGMLR)&quot;,&quot;bigWigLocation&quot;:{&quot;uri&quot;:&quot;https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw&quot;,&quot;locationType&quot;:&quot;UriLocation&quot;}}]}" />
+                    </assert_contents>
+                </extra_files>
             </output>
         </test>
         <test> <!-- Synteny merlin -->
@@ -721,6 +749,11 @@
                                 <param name="annotation_source" value="history" />
                                 <param name="annotation" value="paf/merlun_on_merlon.paf"/>
                             </conditional>
+                            <section name="jbstyle">
+                                <conditional name="track_style">
+                                    <param name="display" value="LinearSyntenyDisplay" />
+                                </conditional>
+                            </section>
                         </conditional>
                     </repeat>
                 </repeat>
@@ -738,6 +771,11 @@
                                 <param name="annotation_source" value="history" />
                                 <param name="annotation" value="paf/merlon_on_merlin.paf"/>
                             </conditional>
+                            <section name="jbstyle">
+                                <conditional name="track_style">
+                                    <param name="display" value="LinearSyntenyDisplay" />
+                                </conditional>
+                            </section>
                         </conditional>
                     </repeat>
                 </repeat>
@@ -760,8 +798,12 @@
                 </repeat>
             </repeat>
             <output name="output">
-                <extra_files name="galaxy.xml" type="file" value="out/03_synteny/galaxy.xml" compare="sim_size" />
-                <extra_files name="config.json" type="file" value="out/03_synteny/config.json" compare="sim_size" />
+                <extra_files name="galaxy.xml" type="file" value="out/03_synteny/galaxy.xml" compare="sim_size" delta="0">
+                    <assert_contents>
+                        <is_valid_xml />
+                    </assert_contents>
+                </extra_files>
+                <extra_files name="config.json" type="file" value="out/03_synteny/config.json" compare="sim_size" delta="0" />
             </output>
         </test>
         <test> <!-- Synteny with remote genomes -->
@@ -779,6 +821,11 @@
                                 <param name="annotation_source" value="history" />
                                 <param name="annotation" value="paf/peach-grape-map.paf"/>
                             </conditional>
+                            <section name="jbstyle">
+                                <conditional name="track_style">
+                                    <param name="display" value="LinearSyntenyDisplay" />
+                                </conditional>
+                            </section>
                         </conditional>
                     </repeat>
                 </repeat>
@@ -791,8 +838,12 @@
                 </conditional>
             </repeat>
             <output name="output">
-                <extra_files name="galaxy.xml" type="file" value="out/04_synteny_remote/galaxy.xml" compare="sim_size" />
-                <extra_files name="config.json" type="file" value="out/04_synteny_remote/config.json" compare="sim_size" />
+                <extra_files name="galaxy.xml" type="file" value="out/04_synteny_remote/galaxy.xml" compare="sim_size" delta="0">
+                    <assert_contents>
+                        <is_valid_xml />
+                    </assert_contents>
+                </extra_files>
+                <extra_files name="config.json" type="file" value="out/04_synteny_remote/config.json" compare="sim_size" delta="0" />
             </output>
         </test>
         <test> <!-- Synteny with remote genomes *and* paf -->
@@ -811,6 +862,11 @@
                                 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/synteny/peach_grape.paf.gz" />
                                 <param name="label" value="Peach vs grape" />
                             </conditional>
+                            <section name="jbstyle">
+                                <conditional name="track_style">
+                                    <param name="display" value="LinearSyntenyDisplay" />
+                                </conditional>
+                            </section>
                         </conditional>
                     </repeat>
                 </repeat>
@@ -823,8 +879,12 @@
                 </conditional>
             </repeat>
             <output name="output">
-                <extra_files name="galaxy.xml" type="file" value="out/05_synteny_full_remote/galaxy.xml" compare="sim_size" />
-                <extra_files name="config.json" type="file" value="out/05_synteny_full_remote/config.json" compare="sim_size" />
+                <extra_files name="galaxy.xml" type="file" value="out/05_synteny_full_remote/galaxy.xml" compare="sim_size" delta="0">
+                    <assert_contents>
+                        <is_valid_xml />
+                    </assert_contents>
+                </extra_files>
+                <extra_files name="config.json" type="file" value="out/05_synteny_full_remote/config.json" compare="sim_size" delta="0" />
             </output>
         </test>
         <test> <!-- various options,  cytobands, ref name aliases -->
@@ -891,8 +951,12 @@
                 <param name="font_size" value="15" />
             </section>
             <output name="output">
-                <extra_files name="galaxy.xml" type="file" value="out/06_various_options/galaxy.xml" compare="sim_size" />
-                <extra_files name="config.json" type="file" value="out/06_various_options/config.json" compare="sim_size" />
+                <extra_files name="galaxy.xml" type="file" value="out/06_various_options/galaxy.xml" compare="sim_size" delta="0">
+                    <assert_contents>
+                        <is_valid_xml />
+                    </assert_contents>
+                </extra_files>
+                <extra_files name="config.json" type="file" value="out/06_various_options/config.json" compare="sim_size" delta="0" />
             </output>
         </test>
         <test> <!-- Synteny, mixed basic / viewer -->
@@ -909,6 +973,11 @@
                                 <param name="annotation_source" value="history" />
                                 <param name="annotation" value="paf/merlun_on_merlon.paf"/>
                             </conditional>
+                            <section name="jbstyle">
+                                <conditional name="track_style">
+                                    <param name="display" value="LinearSyntenyDisplay" />
+                                </conditional>
+                            </section>
                         </conditional>
                     </repeat>
                     <repeat name="data_tracks">
@@ -940,6 +1009,11 @@
                                 <param name="annotation_source" value="history" />
                                 <param name="annotation" value="paf/merlon_on_merlin.paf"/>
                             </conditional>
+                            <section name="jbstyle">
+                                <conditional name="track_style">
+                                    <param name="display" value="LinearSyntenyDisplay" />
+                                </conditional>
+                            </section>
                         </conditional>
                     </repeat>
                     <repeat name="data_tracks">
@@ -976,8 +1050,12 @@
                 </repeat>
             </repeat>
             <output name="output">
-                <extra_files name="galaxy.xml" type="file" value="out/07_synteny_mixed/galaxy.xml" compare="sim_size" />
-                <extra_files name="config.json" type="file" value="out/07_synteny_mixed/config.json" compare="sim_size" />
+                <extra_files name="galaxy.xml" type="file" value="out/07_synteny_mixed/galaxy.xml" compare="sim_size" delta="0">
+                    <assert_contents>
+                        <is_valid_xml />
+                    </assert_contents>
+                </extra_files>
+                <extra_files name="config.json" type="file" value="out/07_synteny_mixed/config.json" compare="sim_size" delta="0" />
             </output>
         </test>
     </tests>
@@ -1016,15 +1094,15 @@
 To add an assembly, you will need to input its sequence, either from a FASTA file in your history
 or from a genome pre-installed by your server administrators.
 
-### Track Groups
+### Track Categories
 
-Track groups represent a set of tracks in a single category. These
+Track Categories represent a set of related tracks. These
 can be used to let your users understand relationships between large
 groups of tracks.
 
-### Annotation Tracks
+### Tracks
 
-Within Track Groups, you have one or more **Annotation Tracks**. Each
+Within Track Categories, you have one or more **Tracks**. Each
 Annotation Track is a dataset, or a group of datasets which have similar styling.
 This allows you to rapidly build up JBrowse instances without having to
 configure tracks individually. For example, if you have five different GFF3 files from
diff -r 93fdd696c281 -r e237edee9a53 macros.xml
--- a/macros.xml	Thu Oct 02 10:20:29 2025 +0000
+++ b/macros.xml	Fri Oct 24 07:50:40 2025 +0000
@@ -11,7 +11,7 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
 
     <xml name="general_options">
         <section name="jbgen" title="Advanced: general JBrowse options" expanded="false">
@@ -223,7 +223,7 @@
             <conditional name="track_style">
                 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
                     <option value="LinearBasicDisplay" selected="true">Basic track display</option>
-                    <option value="LinearSyntenyDisplay" selected="true">Synteny viewer</option>
+                    <option value="LinearSyntenyDisplay">Synteny viewer</option>
                 </param>
                 <when value="LinearBasicDisplay"/>
                 <when value="LinearSyntenyDisplay"/>
diff -r 93fdd696c281 -r e237edee9a53 test-data/gtf/merlin.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf/merlin.gtf	Fri Oct 24 07:50:40 2025 +0000
@@ -0,0 +1,292 @@
+Merlin	merlin	transcript	2	691	.	+	.	transcript_id "Merlin_1_exon"; gene_id "Merlin_1_exon"
+Merlin	merlin	CDS	2	691	.	+	0	transcript_id "Merlin_1_exon";
+Merlin	merlin	transcript	2	691	.	+	.	transcript_id "Merlin_1_mRNA"; gene_id "Merlin_1"
+Merlin	merlin	exon	2	691	.	+	.	transcript_id "Merlin_1_mRNA"; gene_id "Merlin_1";
+Merlin	merlin	transcript	752	1039	.	+	.	transcript_id "Merlin_2_exon"; gene_id "Merlin_2_exon"
+Merlin	merlin	CDS	752	1039	.	+	0	transcript_id "Merlin_2_exon";
+Merlin	merlin	transcript	752	1039	.	+	.	transcript_id "Merlin_2_mRNA"; gene_id "Merlin_2"
+Merlin	merlin	exon	752	1039	.	+	.	transcript_id "Merlin_2_mRNA"; gene_id "Merlin_2";
+Merlin	merlin	transcript	1067	2011	.	-	.	transcript_id "Merlin_3_exon"; gene_id "Merlin_3_exon"
+Merlin	merlin	CDS	1067	2011	.	-	0	transcript_id "Merlin_3_exon";
+Merlin	merlin	transcript	1067	2011	.	-	.	transcript_id "Merlin_3_mRNA"; gene_id "Merlin_3"
+Merlin	merlin	exon	1067	2011	.	-	.	transcript_id "Merlin_3_mRNA"; gene_id "Merlin_3";
+Merlin	merlin	transcript	2011	3066	.	-	.	transcript_id "Merlin_4_exon"; gene_id "Merlin_4_exon"
+Merlin	merlin	CDS	2011	3066	.	-	0	transcript_id "Merlin_4_exon";
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+Merlin	merlin	transcript	46527	47255	.	+	.	transcript_id "Merlin_51_mRNA"; gene_id "Merlin_51"
+Merlin	merlin	exon	46527	47255	.	+	.	transcript_id "Merlin_51_mRNA"; gene_id "Merlin_51";
+Merlin	merlin	transcript	47252	47485	.	+	.	transcript_id "Merlin_52_exon"; gene_id "Merlin_52_exon"
+Merlin	merlin	CDS	47252	47485	.	+	0	transcript_id "Merlin_52_exon";
+Merlin	merlin	transcript	47252	47485	.	+	.	transcript_id "Merlin_52_mRNA"; gene_id "Merlin_52"
+Merlin	merlin	exon	47252	47485	.	+	.	transcript_id "Merlin_52_mRNA"; gene_id "Merlin_52";
+Merlin	merlin	transcript	47485	47940	.	+	.	transcript_id "Merlin_53_exon"; gene_id "Merlin_53_exon"
+Merlin	merlin	CDS	47485	47940	.	+	0	transcript_id "Merlin_53_exon";
+Merlin	merlin	transcript	47485	47940	.	+	.	transcript_id "Merlin_53_mRNA"; gene_id "Merlin_53"
+Merlin	merlin	exon	47485	47940	.	+	.	transcript_id "Merlin_53_mRNA"; gene_id "Merlin_53";
+Merlin	merlin	transcript	47937	48143	.	+	.	transcript_id "Merlin_54_exon"; gene_id "Merlin_54_exon"
+Merlin	merlin	CDS	47937	48143	.	+	0	transcript_id "Merlin_54_exon";
+Merlin	merlin	transcript	47937	48143	.	+	.	transcript_id "Merlin_54_mRNA"; gene_id "Merlin_54"
+Merlin	merlin	exon	47937	48143	.	+	.	transcript_id "Merlin_54_mRNA"; gene_id "Merlin_54";
+Merlin	merlin	transcript	48140	48358	.	+	.	transcript_id "Merlin_55_exon"; gene_id "Merlin_55_exon"
+Merlin	merlin	CDS	48140	48358	.	+	0	transcript_id "Merlin_55_exon";
+Merlin	merlin	transcript	48140	48358	.	+	.	transcript_id "Merlin_55_mRNA"; gene_id "Merlin_55"
+Merlin	merlin	exon	48140	48358	.	+	.	transcript_id "Merlin_55_mRNA"; gene_id "Merlin_55";
+Merlin	merlin	transcript	48418	48600	.	+	.	transcript_id "Merlin_56_exon"; gene_id "Merlin_56_exon"
+Merlin	merlin	CDS	48418	48600	.	+	0	transcript_id "Merlin_56_exon";
+Merlin	merlin	transcript	48418	48600	.	+	.	transcript_id "Merlin_56_mRNA"; gene_id "Merlin_56"
+Merlin	merlin	exon	48418	48600	.	+	.	transcript_id "Merlin_56_mRNA"; gene_id "Merlin_56";
+Merlin	merlin	transcript	48584	48769	.	+	.	transcript_id "Merlin_57_exon"; gene_id "Merlin_57_exon"
+Merlin	merlin	CDS	48584	48769	.	+	0	transcript_id "Merlin_57_exon";
+Merlin	merlin	transcript	48584	48769	.	+	.	transcript_id "Merlin_57_mRNA"; gene_id "Merlin_57"
+Merlin	merlin	exon	48584	48769	.	+	.	transcript_id "Merlin_57_mRNA"; gene_id "Merlin_57";
+Merlin	merlin	transcript	48826	49053	.	+	.	transcript_id "Merlin_58_exon"; gene_id "Merlin_58_exon"
+Merlin	merlin	CDS	48826	49053	.	+	0	transcript_id "Merlin_58_exon";
+Merlin	merlin	transcript	48826	49053	.	+	.	transcript_id "Merlin_58_mRNA"; gene_id "Merlin_58"
+Merlin	merlin	exon	48826	49053	.	+	.	transcript_id "Merlin_58_mRNA"; gene_id "Merlin_58";
+Merlin	merlin	transcript	49076	49432	.	+	.	transcript_id "Merlin_59_exon"; gene_id "Merlin_59_exon"
+Merlin	merlin	CDS	49076	49432	.	+	0	transcript_id "Merlin_59_exon";
+Merlin	merlin	transcript	49076	49432	.	+	.	transcript_id "Merlin_59_mRNA"; gene_id "Merlin_59"
+Merlin	merlin	exon	49076	49432	.	+	.	transcript_id "Merlin_59_mRNA"; gene_id "Merlin_59";
+Merlin	merlin	transcript	49844	50110	.	+	.	transcript_id "Merlin_60_exon"; gene_id "Merlin_60_exon"
+Merlin	merlin	CDS	49844	50110	.	+	0	transcript_id "Merlin_60_exon";
+Merlin	merlin	transcript	49844	50110	.	+	.	transcript_id "Merlin_60_mRNA"; gene_id "Merlin_60"
+Merlin	merlin	exon	49844	50110	.	+	.	transcript_id "Merlin_60_mRNA"; gene_id "Merlin_60";
+Merlin	merlin	transcript	50983	51234	.	+	.	transcript_id "Merlin_61_exon"; gene_id "Merlin_61_exon"
+Merlin	merlin	CDS	50983	51234	.	+	0	transcript_id "Merlin_61_exon";
+Merlin	merlin	transcript	50983	51234	.	+	.	transcript_id "Merlin_61_mRNA"; gene_id "Merlin_61"
+Merlin	merlin	exon	50983	51234	.	+	.	transcript_id "Merlin_61_mRNA"; gene_id "Merlin_61";
+Merlin	merlin	transcript	51596	51838	.	+	.	transcript_id "Merlin_62_exon"; gene_id "Merlin_62_exon"
+Merlin	merlin	CDS	51596	51838	.	+	0	transcript_id "Merlin_62_exon";
+Merlin	merlin	transcript	51596	51838	.	+	.	transcript_id "Merlin_62_mRNA"; gene_id "Merlin_62"
+Merlin	merlin	exon	51596	51838	.	+	.	transcript_id "Merlin_62_mRNA"; gene_id "Merlin_62";
+Merlin	merlin	transcript	51835	52182	.	+	.	transcript_id "Merlin_63_exon"; gene_id "Merlin_63_exon"
+Merlin	merlin	CDS	51835	52182	.	+	0	transcript_id "Merlin_63_exon";
+Merlin	merlin	transcript	51835	52182	.	+	.	transcript_id "Merlin_63_mRNA"; gene_id "Merlin_63"
+Merlin	merlin	exon	51835	52182	.	+	.	transcript_id "Merlin_63_mRNA"; gene_id "Merlin_63";
+Merlin	merlin	transcript	52175	52684	.	+	.	transcript_id "Merlin_64_exon"; gene_id "Merlin_64_exon"
+Merlin	merlin	CDS	52175	52684	.	+	0	transcript_id "Merlin_64_exon";
+Merlin	merlin	transcript	52175	52684	.	+	.	transcript_id "Merlin_64_mRNA"; gene_id "Merlin_64"
+Merlin	merlin	exon	52175	52684	.	+	.	transcript_id "Merlin_64_mRNA"; gene_id "Merlin_64";
+Merlin	merlin	transcript	52681	52827	.	+	.	transcript_id "Merlin_65_exon"; gene_id "Merlin_65_exon"
+Merlin	merlin	CDS	52681	52827	.	+	0	transcript_id "Merlin_65_exon";
+Merlin	merlin	transcript	52681	52827	.	+	.	transcript_id "Merlin_65_mRNA"; gene_id "Merlin_65"
+Merlin	merlin	exon	52681	52827	.	+	.	transcript_id "Merlin_65_mRNA"; gene_id "Merlin_65";
+Merlin	merlin	transcript	52806	53030	.	+	.	transcript_id "Merlin_66_exon"; gene_id "Merlin_66_exon"
+Merlin	merlin	CDS	52806	53030	.	+	0	transcript_id "Merlin_66_exon";
+Merlin	merlin	transcript	52806	53030	.	+	.	transcript_id "Merlin_66_mRNA"; gene_id "Merlin_66"
+Merlin	merlin	exon	52806	53030	.	+	.	transcript_id "Merlin_66_mRNA"; gene_id "Merlin_66";
+Merlin	merlin	transcript	53032	53475	.	+	.	transcript_id "Merlin_67_exon"; gene_id "Merlin_67_exon"
+Merlin	merlin	CDS	53032	53475	.	+	0	transcript_id "Merlin_67_exon";
+Merlin	merlin	transcript	53032	53475	.	+	.	transcript_id "Merlin_67_mRNA"; gene_id "Merlin_67"
+Merlin	merlin	exon	53032	53475	.	+	.	transcript_id "Merlin_67_mRNA"; gene_id "Merlin_67";
+Merlin	merlin	transcript	53647	54225	.	+	.	transcript_id "Merlin_68_exon"; gene_id "Merlin_68_exon"
+Merlin	merlin	CDS	53647	54225	.	+	0	transcript_id "Merlin_68_exon";
+Merlin	merlin	transcript	53647	54225	.	+	.	transcript_id "Merlin_68_mRNA"; gene_id "Merlin_68"
+Merlin	merlin	exon	53647	54225	.	+	.	transcript_id "Merlin_68_mRNA"; gene_id "Merlin_68";
+Merlin	merlin	transcript	54316	54516	.	+	.	transcript_id "Merlin_69_exon"; gene_id "Merlin_69_exon"
+Merlin	merlin	CDS	54316	54516	.	+	0	transcript_id "Merlin_69_exon";
+Merlin	merlin	transcript	54316	54516	.	+	.	transcript_id "Merlin_69_mRNA"; gene_id "Merlin_69"
+Merlin	merlin	exon	54316	54516	.	+	.	transcript_id "Merlin_69_mRNA"; gene_id "Merlin_69";
+Merlin	merlin	transcript	54569	55168	.	+	.	transcript_id "Merlin_70_exon"; gene_id "Merlin_70_exon"
+Merlin	merlin	CDS	54569	55168	.	+	0	transcript_id "Merlin_70_exon";
+Merlin	merlin	transcript	54569	55168	.	+	.	transcript_id "Merlin_70_mRNA"; gene_id "Merlin_70"
+Merlin	merlin	exon	54569	55168	.	+	.	transcript_id "Merlin_70_mRNA"; gene_id "Merlin_70";
+Merlin	merlin	transcript	55216	55860	.	+	.	transcript_id "Merlin_71_exon"; gene_id "Merlin_71_exon"
+Merlin	merlin	CDS	55216	55860	.	+	0	transcript_id "Merlin_71_exon";
+Merlin	merlin	transcript	55216	55860	.	+	.	transcript_id "Merlin_71_mRNA"; gene_id "Merlin_71"
+Merlin	merlin	exon	55216	55860	.	+	.	transcript_id "Merlin_71_mRNA"; gene_id "Merlin_71";
+Merlin	merlin	transcript	55857	56279	.	+	.	transcript_id "Merlin_72_exon"; gene_id "Merlin_72_exon"
+Merlin	merlin	CDS	55857	56279	.	+	0	transcript_id "Merlin_72_exon";
+Merlin	merlin	transcript	55857	56279	.	+	.	transcript_id "Merlin_72_mRNA"; gene_id "Merlin_72"
+Merlin	merlin	exon	55857	56279	.	+	.	transcript_id "Merlin_72_mRNA"; gene_id "Merlin_72";
+Merlin	merlin	transcript	56276	56644	.	+	.	transcript_id "Merlin_73_exon"; gene_id "Merlin_73_exon"
+Merlin	merlin	CDS	56276	56644	.	+	0	transcript_id "Merlin_73_exon";
+Merlin	merlin	transcript	56276	56644	.	+	.	transcript_id "Merlin_73_mRNA"; gene_id "Merlin_73"
+Merlin	merlin	exon	56276	56644	.	+	.	transcript_id "Merlin_73_mRNA"; gene_id "Merlin_73";
diff -r 93fdd696c281 -r e237edee9a53 test-data/out/01_all_tracks/config.json
--- a/test-data/out/01_all_tracks/config.json	Thu Oct 02 10:20:29 2025 +0000
+++ b/test-data/out/01_all_tracks/config.json	Fri Oct 24 07:50:40 2025 +0000
@@ -55,18 +55,19 @@
           "assembly": "merlin.fa",
           "loc": "Merlin",
           "tracks": [
-            "6843cfc92b274808c8baa5a15cab5855_0_0",
-            "902614424ab2f62ce4edd6a978b2a71f_1_0",
-            "6b7dbed6d89698464c37243cb7a711de_1_1",
-            "793abf2f5fb78801c2863e040ad7c658_2_0",
-            "d9f3b09a4719c3b0b6cca3f73de6f425_3_0",
-            "c48d88e425802c8d168ec01575c6c43a_4_0",
-            "08ddbbfb7c03c6b254db206a6415cc2a_5_0",
-            "96b0beda20fb7fb90960ad5024a7a97a_5_1",
-            "7dffd3bd033fc065c4a413aa9bfa4899_6_0",
-            "7381e3e08a3fe229fa516fc0abf20950_7_0",
-            "0448d8682eef9e71183fbc9b84962afa_8_0",
-            "936a5285fbedf1c37f5daf26837035b2_9_0"
+            "a7e8fe627b3e52b4c1f8c3c886aa9e57_0_0",
+            "da7c1329ab838dfaeee1703c013a5bc0_1_0",
+            "f2b6c4173397b6b812014c2b32e822a1_2_0",
+            "dd9f9b6093c48d07509eee6176e1bb1a_2_1",
+            "c488f0dd81de5234363870aac1b6099e_3_0",
+            "48ffd6161c7eec8f82482fb614f08d13_4_0",
+            "8f850b3775e54706acf8e3ae3856c21e_5_0",
+            "f04ae7e29a15ee551a3d5cb1b7df6d9f_6_0",
+            "69acdc3612406c3cb0347062091c4228_6_1",
+            "780b1598e6368efa353cc705c9d08ab3_7_0",
+            "f329aa022d2aa8aea5316bfa9c7cc113_8_0",
+            "74b81aa00dec3d38a9ac2a1176c3cc7e_9_0",
+            "936a5285fbedf1c37f5daf26837035b2_10_0"
           ]
         }
       }
@@ -75,17 +76,17 @@
   "tracks": [
     {
       "type": "FeatureTrack",
-      "trackId": "6843cfc92b274808c8baa5a15cab5855_0_0",
+      "trackId": "a7e8fe627b3e52b4c1f8c3c886aa9e57_0_0",
       "name": "merlin.gff",
       "adapter": {
         "type": "Gff3TabixAdapter",
         "gffGzLocation": {
-          "uri": "data/6843cfc92b274808c8baa5a15cab5855_0_0.gff.gz",
+          "uri": "data/a7e8fe627b3e52b4c1f8c3c886aa9e57_0_0.gff.gz",
           "locationType": "UriLocation"
         },
         "index": {
           "location": {
-            "uri": "data/6843cfc92b274808c8baa5a15cab5855_0_0.gff.gz.tbi",
+            "uri": "data/a7e8fe627b3e52b4c1f8c3c886aa9e57_0_0.gff.gz.tbi",
             "locationType": "UriLocation"
           },
           "indexType": "TBI"
@@ -100,7 +101,66 @@
       "displays": [
         {
           "type": "LinearBasicDisplay",
-          "displayId": "6843cfc92b274808c8baa5a15cab5855_0_0_LinearBasicDisplay",
+          "displayId": "a7e8fe627b3e52b4c1f8c3c886aa9e57_0_0_LinearBasicDisplay",
+          "renderer": {
+            "type": "SvgFeatureRenderer",
+            "showLabels": true,
+            "showDescriptions": true,
+            "labels": {
+              "name": "jexl:get(feature,'name') || get(feature,'id')",
+              "description": "jexl:get(feature,'note') || get(feature,'description')"
+            },
+            "displayMode": "normal",
+            "maxHeight": 600
+          }
+        }
+      ],
+      "formatDetails": {
+        "depth": 1
+      },
+      "metadata": {
+        "dataset_id": "2a23db38ccbbc7de",
+        "dataset_hid": "2",
+        "dataset_size": "110.3 KB",
+        "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_1975\">gff3</a>",
+        "dataset_file_ext": "gff3",
+        "history_id": "4d30d636fed0a9f6",
+        "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
+        "history_user_id": "1",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/4d30d636fed0a9f6\">Tool Test History for jbrowse2/3.6.5+galaxy1-0</a>",
+        "metadata_dbkey": "?",
+        "metadata_data_lines": "1228",
+        "metadata_comment_lines": "2",
+        "metadata_columns": "9",
+        "metadata_column_names": "[]",
+        "metadata_delimiter": "\t",
+        "metadata_attributes": "4",
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/2a23db38ccbbc7de/show_params\">__DATA_FETCH__</a>"
+      }
+    },
+    {
+      "type": "FeatureTrack",
+      "trackId": "da7c1329ab838dfaeee1703c013a5bc0_1_0",
+      "name": "merlin.gtf",
+      "adapter": {
+        "type": "GtfAdapter",
+        "gtfLocation": {
+          "uri": "data/da7c1329ab838dfaeee1703c013a5bc0_1_0.gtf",
+          "locationType": "UriLocation"
+        }
+      },
+      "category": [
+        "Default"
+      ],
+      "assemblyNames": [
+        "merlin.fa"
+      ],
+      "displays": [
+        {
+          "type": "LinearBasicDisplay",
+          "displayId": "da7c1329ab838dfaeee1703c013a5bc0_1_0_LinearBasicDisplay",
           "renderer": {
             "type": "SvgFeatureRenderer",
             "showLabels": true,
@@ -118,40 +178,40 @@
         "depth": 1
       },
       "metadata": {
-        "dataset_id": "33b9ecfea4207697",
-        "dataset_hid": "2",
-        "dataset_size": "110.3 KB",
-        "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_1975\">gff3</a>",
-        "dataset_file_ext": "gff3",
-        "history_id": "ffb0709d52bfbdea",
+        "dataset_id": "0b7812b25f4cfb76",
+        "dataset_hid": "3",
+        "dataset_size": "25.0 KB",
+        "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2306\">gtf</a>",
+        "dataset_file_ext": "gtf",
+        "history_id": "4d30d636fed0a9f6",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/ffb0709d52bfbdea\">Tool Test History for jbrowse2/3.6.5+galaxy0-0</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/4d30d636fed0a9f6\">Tool Test History for jbrowse2/3.6.5+galaxy1-0</a>",
         "metadata_dbkey": "?",
-        "metadata_data_lines": "1228",
-        "metadata_comment_lines": "2",
+        "metadata_data_lines": "292",
+        "metadata_comment_lines": "0",
         "metadata_columns": "9",
         "metadata_column_names": "[]",
-        "metadata_delimiter": "__tc__",
-        "metadata_attributes": "4",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/33b9ecfea4207697/show_params\">upload1</a>"
+        "metadata_delimiter": "\t",
+        "metadata_attributes": "2",
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/0b7812b25f4cfb76/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "FeatureTrack",
-      "trackId": "902614424ab2f62ce4edd6a978b2a71f_1_0",
+      "trackId": "f2b6c4173397b6b812014c2b32e822a1_2_0",
       "name": "test-3.bed",
       "adapter": {
         "type": "BedTabixAdapter",
         "bedGzLocation": {
-          "uri": "data/902614424ab2f62ce4edd6a978b2a71f_1_0.bed.gz",
+          "uri": "data/f2b6c4173397b6b812014c2b32e822a1_2_0.bed.gz",
           "locationType": "UriLocation"
         },
         "index": {
           "location": {
-            "uri": "data/902614424ab2f62ce4edd6a978b2a71f_1_0.bed.gz.tbi",
+            "uri": "data/f2b6c4173397b6b812014c2b32e822a1_2_0.bed.gz.tbi",
             "locationType": "UriLocation"
           },
           "indexType": "TBI"
@@ -166,7 +226,7 @@
       "displays": [
         {
           "type": "LinearBasicDisplay",
-          "displayId": "902614424ab2f62ce4edd6a978b2a71f_1_0_LinearBasicDisplay",
+          "displayId": "f2b6c4173397b6b812014c2b32e822a1_2_0_LinearBasicDisplay",
           "renderer": {
             "type": "SvgFeatureRenderer",
             "showLabels": true,
@@ -184,44 +244,45 @@
         "depth": 1
       },
       "metadata": {
-        "dataset_id": "dad64ae4d71c7372",
-        "dataset_hid": "3",
+        "dataset_id": "bd91a97d652fafe1",
+        "dataset_hid": "4",
         "dataset_size": "49 bytes",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_3003\">bed</a>",
         "dataset_file_ext": "bed",
-        "history_id": "ffb0709d52bfbdea",
+        "history_id": "4d30d636fed0a9f6",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/ffb0709d52bfbdea\">Tool Test History for jbrowse2/3.6.5+galaxy0-0</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/4d30d636fed0a9f6\">Tool Test History for jbrowse2/3.6.5+galaxy1-0</a>",
         "metadata_dbkey": "?",
         "metadata_data_lines": "3",
         "metadata_comment_lines": "0",
         "metadata_columns": "3",
         "metadata_column_names": "[]",
-        "metadata_delimiter": "__tc__",
+        "metadata_delimiter": "\t",
         "metadata_chromCol": "1",
         "metadata_startCol": "2",
         "metadata_endCol": "3",
         "metadata_strandCol": "0",
-        "metadata_viz_filter_cols": "[4]",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/dad64ae4d71c7372/show_params\">upload1</a>"
+        "metadata_nameCol": "0",
+        "metadata_viz_filter_cols": "4",
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/bd91a97d652fafe1/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "FeatureTrack",
-      "trackId": "6b7dbed6d89698464c37243cb7a711de_1_1",
+      "trackId": "dd9f9b6093c48d07509eee6176e1bb1a_2_1",
       "name": "test-6.bed",
       "adapter": {
         "type": "BedTabixAdapter",
         "bedGzLocation": {
-          "uri": "data/6b7dbed6d89698464c37243cb7a711de_1_1.bed.gz",
+          "uri": "data/dd9f9b6093c48d07509eee6176e1bb1a_2_1.bed.gz",
           "locationType": "UriLocation"
         },
         "index": {
           "location": {
-            "uri": "data/6b7dbed6d89698464c37243cb7a711de_1_1.bed.gz.tbi",
+            "uri": "data/dd9f9b6093c48d07509eee6176e1bb1a_2_1.bed.gz.tbi",
             "locationType": "UriLocation"
           },
           "indexType": "TBI"
@@ -236,7 +297,7 @@
       "displays": [
         {
           "type": "LinearBasicDisplay",
-          "displayId": "6b7dbed6d89698464c37243cb7a711de_1_1_LinearBasicDisplay",
+          "displayId": "dd9f9b6093c48d07509eee6176e1bb1a_2_1_LinearBasicDisplay",
           "renderer": {
             "type": "SvgFeatureRenderer",
             "showLabels": true,
@@ -254,44 +315,45 @@
         "depth": 1
       },
       "metadata": {
-        "dataset_id": "36cc4ad69bb5f2a1",
-        "dataset_hid": "4",
+        "dataset_id": "3aa468ce9e79eed2",
+        "dataset_hid": "5",
         "dataset_size": "180 bytes",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_3003\">bed</a>",
         "dataset_file_ext": "bed",
-        "history_id": "ffb0709d52bfbdea",
+        "history_id": "4d30d636fed0a9f6",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/ffb0709d52bfbdea\">Tool Test History for jbrowse2/3.6.5+galaxy0-0</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/4d30d636fed0a9f6\">Tool Test History for jbrowse2/3.6.5+galaxy1-0</a>",
         "metadata_dbkey": "?",
         "metadata_data_lines": "3",
         "metadata_comment_lines": "0",
         "metadata_columns": "6",
         "metadata_column_names": "[]",
-        "metadata_delimiter": "__tc__",
+        "metadata_delimiter": "\t",
         "metadata_chromCol": "1",
         "metadata_startCol": "2",
         "metadata_endCol": "3",
         "metadata_strandCol": "6",
-        "metadata_viz_filter_cols": "[4]",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/36cc4ad69bb5f2a1/show_params\">upload1</a>"
+        "metadata_nameCol": "4",
+        "metadata_viz_filter_cols": "4",
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/3aa468ce9e79eed2/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "AlignmentsTrack",
-      "trackId": "793abf2f5fb78801c2863e040ad7c658_2_0",
+      "trackId": "c488f0dd81de5234363870aac1b6099e_3_0",
       "name": "merlin-sample.bam",
       "adapter": {
         "type": "BamAdapter",
         "bamLocation": {
-          "uri": "data/793abf2f5fb78801c2863e040ad7c658_2_0.bam",
+          "uri": "data/c488f0dd81de5234363870aac1b6099e_3_0.bam",
           "locationType": "UriLocation"
         },
         "index": {
           "location": {
-            "uri": "data/793abf2f5fb78801c2863e040ad7c658_2_0.bam.bai",
+            "uri": "data/c488f0dd81de5234363870aac1b6099e_3_0.bam.bai",
             "locationType": "UriLocation"
           },
           "indexType": "BAI"
@@ -321,42 +383,41 @@
       "displays": [
         {
           "type": "LinearAlignmentsDisplay",
-          "displayId": "793abf2f5fb78801c2863e040ad7c658_2_0_LinearAlignmentsDisplay"
+          "displayId": "c488f0dd81de5234363870aac1b6099e_3_0_LinearAlignmentsDisplay"
         }
       ],
       "metadata": {
-        "dataset_id": "ea3d8239d386c6a4",
-        "dataset_hid": "5",
+        "dataset_id": "c8d274edba5d366b",
+        "dataset_hid": "6",
         "dataset_size": "12.9 KB",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2572\">bam</a>",
         "dataset_file_ext": "bam",
-        "history_id": "ffb0709d52bfbdea",
+        "history_id": "4d30d636fed0a9f6",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/ffb0709d52bfbdea\">Tool Test History for jbrowse2/3.6.5+galaxy0-0</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/4d30d636fed0a9f6\">Tool Test History for jbrowse2/3.6.5+galaxy1-0</a>",
         "metadata_dbkey": "?",
         "metadata_columns": "12",
-        "metadata_column_names": "[\"QNAME\", \"FLAG\", \"RNAME\", \"POS\", \"MAPQ\", \"CIGAR\", \"MRNM\", \"MPOS\", \"ISIZE\", \"SEQ\", \"QUAL\", \"OPT\"]",
+        "metadata_column_names": "['QNAME', 'FLAG', 'RNAME', 'POS', 'MAPQ', 'CIGAR', 'MRNM', 'MPOS', 'ISIZE', 'SEQ', 'QUAL', 'OPT']",
         "metadata_bam_version": "1.3",
         "metadata_sort_order": "coordinate",
         "metadata_read_groups": "[]",
-        "metadata_reference_names": "[\"Merlin\"]",
+        "metadata_reference_names": "['Merlin']",
         "metadata_reference_lengths": "[172788]",
-        "metadata_bam_header": "{\"HD\": {\"SO\": \"coordinate\", \"VN\": \"1.3\"}, \"PG\": [{\"CL\": \"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\", \"ID\": \"minimap2\", \"PN\": \"minimap2\", \"VN\": \"2.5-r572\"}], \"SQ\": [{\"LN\": 172788, \"SN\": \"Merlin\"}]}",
-        "metadata_bam_index": "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/ea3d8239d386c6a4/show_params\">upload1</a>"
+        "metadata_bam_header": "{'HD': {'SO': 'coordinate', 'VN': '1.3'}, 'PG': [{'CL': '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', 'ID': 'minimap2', 'PN': 'minimap2', 'VN': '2.5-r572'}], 'SQ': [{'LN': 172788, 'SN': 'Merlin'}]}",
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/c8d274edba5d366b/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "QuantitativeTrack",
-      "trackId": "d9f3b09a4719c3b0b6cca3f73de6f425_3_0",
+      "trackId": "48ffd6161c7eec8f82482fb614f08d13_4_0",
       "name": "data.bw",
       "adapter": {
         "type": "BigWigAdapter",
         "bigWigLocation": {
-          "uri": "data/d9f3b09a4719c3b0b6cca3f73de6f425_3_0.bw",
+          "uri": "data/48ffd6161c7eec8f82482fb614f08d13_4_0.bw",
           "locationType": "UriLocation"
         }
       },
@@ -369,38 +430,38 @@
       "displays": [
         {
           "type": "LinearWiggleDisplay",
-          "displayId": "d9f3b09a4719c3b0b6cca3f73de6f425_3_0_LinearWiggleDisplay",
+          "displayId": "48ffd6161c7eec8f82482fb614f08d13_4_0_LinearWiggleDisplay",
           "defaultRendering": "xyplot"
         }
       ],
       "metadata": {
-        "dataset_id": "d753b8dba6e25d09",
-        "dataset_hid": "8",
+        "dataset_id": "2f8b42de958784ae",
+        "dataset_hid": "7",
         "dataset_size": "81.6 KB",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_3006\">bigwig</a>",
         "dataset_file_ext": "bigwig",
-        "history_id": "ffb0709d52bfbdea",
+        "history_id": "4d30d636fed0a9f6",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/ffb0709d52bfbdea\">Tool Test History for jbrowse2/3.6.5+galaxy0-0</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/4d30d636fed0a9f6\">Tool Test History for jbrowse2/3.6.5+galaxy1-0</a>",
         "metadata_dbkey": "?",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/d753b8dba6e25d09/show_params\">upload1</a>"
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/2f8b42de958784ae/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "AlignmentsTrack",
-      "trackId": "c48d88e425802c8d168ec01575c6c43a_4_0",
+      "trackId": "8f850b3775e54706acf8e3ae3856c21e_5_0",
       "name": "merlin-sample.cram",
       "adapter": {
         "type": "CramAdapter",
         "cramLocation": {
-          "uri": "data/c48d88e425802c8d168ec01575c6c43a_4_0.cram",
+          "uri": "data/8f850b3775e54706acf8e3ae3856c21e_5_0.cram",
           "locationType": "UriLocation"
         },
         "craiLocation": {
-          "uri": "data/c48d88e425802c8d168ec01575c6c43a_4_0.cram.crai",
+          "uri": "data/8f850b3775e54706acf8e3ae3856c21e_5_0.cram.crai",
           "locationType": "UriLocation"
         },
         "sequenceAdapter": {
@@ -428,35 +489,34 @@
       "displays": [
         {
           "type": "LinearAlignmentsDisplay",
-          "displayId": "c48d88e425802c8d168ec01575c6c43a_4_0_LinearAlignmentsDisplay"
+          "displayId": "8f850b3775e54706acf8e3ae3856c21e_5_0_LinearAlignmentsDisplay"
         }
       ],
       "metadata": {
-        "dataset_id": "1f72eafab720ae62",
-        "dataset_hid": "7",
+        "dataset_id": "76ca3a0a3de24f95",
+        "dataset_hid": "8",
         "dataset_size": "8.3 KB",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_3462\">cram</a>",
         "dataset_file_ext": "cram",
-        "history_id": "ffb0709d52bfbdea",
+        "history_id": "4d30d636fed0a9f6",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/ffb0709d52bfbdea\">Tool Test History for jbrowse2/3.6.5+galaxy0-0</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/4d30d636fed0a9f6\">Tool Test History for jbrowse2/3.6.5+galaxy1-0</a>",
         "metadata_dbkey": "?",
         "metadata_cram_version": "3.0",
-        "metadata_cram_index": "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/1f72eafab720ae62/show_params\">upload1</a>"
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/76ca3a0a3de24f95/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "QuantitativeTrack",
-      "trackId": "08ddbbfb7c03c6b254db206a6415cc2a_5_0",
+      "trackId": "f04ae7e29a15ee551a3d5cb1b7df6d9f_6_0",
       "name": "data.bw",
       "adapter": {
         "type": "BigWigAdapter",
         "bigWigLocation": {
-          "uri": "data/08ddbbfb7c03c6b254db206a6415cc2a_5_0.bw",
+          "uri": "data/f04ae7e29a15ee551a3d5cb1b7df6d9f_6_0.bw",
           "locationType": "UriLocation"
         }
       },
@@ -469,34 +529,34 @@
       "displays": [
         {
           "type": "LinearWiggleDisplay",
-          "displayId": "08ddbbfb7c03c6b254db206a6415cc2a_5_0_LinearWiggleDisplay",
+          "displayId": "f04ae7e29a15ee551a3d5cb1b7df6d9f_6_0_LinearWiggleDisplay",
           "defaultRendering": "xyplot"
         }
       ],
       "metadata": {
-        "dataset_id": "d753b8dba6e25d09",
-        "dataset_hid": "8",
+        "dataset_id": "2f8b42de958784ae",
+        "dataset_hid": "7",
         "dataset_size": "81.6 KB",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_3006\">bigwig</a>",
         "dataset_file_ext": "bigwig",
-        "history_id": "ffb0709d52bfbdea",
+        "history_id": "4d30d636fed0a9f6",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/ffb0709d52bfbdea\">Tool Test History for jbrowse2/3.6.5+galaxy0-0</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/4d30d636fed0a9f6\">Tool Test History for jbrowse2/3.6.5+galaxy1-0</a>",
         "metadata_dbkey": "?",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/d753b8dba6e25d09/show_params\">upload1</a>"
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/2f8b42de958784ae/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "QuantitativeTrack",
-      "trackId": "96b0beda20fb7fb90960ad5024a7a97a_5_1",
+      "trackId": "69acdc3612406c3cb0347062091c4228_6_1",
       "name": "smaller2.bw",
       "adapter": {
         "type": "BigWigAdapter",
         "bigWigLocation": {
-          "uri": "data/96b0beda20fb7fb90960ad5024a7a97a_5_1.bw",
+          "uri": "data/69acdc3612406c3cb0347062091c4228_6_1.bw",
           "locationType": "UriLocation"
         }
       },
@@ -509,39 +569,39 @@
       "displays": [
         {
           "type": "LinearWiggleDisplay",
-          "displayId": "96b0beda20fb7fb90960ad5024a7a97a_5_1_LinearWiggleDisplay",
+          "displayId": "69acdc3612406c3cb0347062091c4228_6_1_LinearWiggleDisplay",
           "defaultRendering": "xyplot"
         }
       ],
       "metadata": {
-        "dataset_id": "ee963fc82e556fe8",
+        "dataset_id": "fff5871153f6d061",
         "dataset_hid": "9",
         "dataset_size": "10.9 KB",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_3006\">bigwig</a>",
         "dataset_file_ext": "bigwig",
-        "history_id": "ffb0709d52bfbdea",
+        "history_id": "4d30d636fed0a9f6",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/ffb0709d52bfbdea\">Tool Test History for jbrowse2/3.6.5+galaxy0-0</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/4d30d636fed0a9f6\">Tool Test History for jbrowse2/3.6.5+galaxy1-0</a>",
         "metadata_dbkey": "?",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/ee963fc82e556fe8/show_params\">upload1</a>"
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/fff5871153f6d061/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "VariantTrack",
-      "trackId": "7dffd3bd033fc065c4a413aa9bfa4899_6_0",
+      "trackId": "780b1598e6368efa353cc705c9d08ab3_7_0",
       "name": "test.vcf",
       "adapter": {
         "type": "VcfTabixAdapter",
         "vcfGzLocation": {
-          "uri": "data/7dffd3bd033fc065c4a413aa9bfa4899_6_0.vcf.gz",
+          "uri": "data/780b1598e6368efa353cc705c9d08ab3_7_0.vcf.gz",
           "locationType": "UriLocation"
         },
         "index": {
           "location": {
-            "uri": "data/7dffd3bd033fc065c4a413aa9bfa4899_6_0.vcf.gz.tbi",
+            "uri": "data/780b1598e6368efa353cc705c9d08ab3_7_0.vcf.gz.tbi",
             "locationType": "UriLocation"
           },
           "indexType": "TBI"
@@ -556,41 +616,41 @@
       "displays": [
         {
           "type": "LinearVariantDisplay",
-          "displayId": "7dffd3bd033fc065c4a413aa9bfa4899_6_0_LinearVariantDisplay"
+          "displayId": "780b1598e6368efa353cc705c9d08ab3_7_0_LinearVariantDisplay"
         }
       ],
       "formatDetails": {},
       "metadata": {
-        "dataset_id": "2a8101cbb778a3ae",
+        "dataset_id": "d68659e09db1368d",
         "dataset_hid": "10",
         "dataset_size": "1.5 KB",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_3016\">vcf</a>",
         "dataset_file_ext": "vcf",
-        "history_id": "ffb0709d52bfbdea",
+        "history_id": "4d30d636fed0a9f6",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/ffb0709d52bfbdea\">Tool Test History for jbrowse2/3.6.5+galaxy0-0</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/4d30d636fed0a9f6\">Tool Test History for jbrowse2/3.6.5+galaxy1-0</a>",
         "metadata_dbkey": "?",
         "metadata_data_lines": "5",
         "metadata_comment_lines": "18",
         "metadata_columns": "12",
         "metadata_column_names": "[]",
-        "metadata_delimiter": "__tc__",
-        "metadata_viz_filter_cols": "[5]",
-        "metadata_sample_names": "[\"NA00001\", \"NA00002\", \"NA00003\"]",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/2a8101cbb778a3ae/show_params\">upload1</a>"
+        "metadata_delimiter": "\t",
+        "metadata_viz_filter_cols": "5",
+        "metadata_sample_names": "['NA00001', 'NA00002', 'NA00003']",
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/d68659e09db1368d/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "HicTrack",
-      "trackId": "7381e3e08a3fe229fa516fc0abf20950_7_0",
+      "trackId": "f329aa022d2aa8aea5316bfa9c7cc113_8_0",
       "name": "merlin.hic",
       "adapter": {
         "type": "HicAdapter",
         "hicLocation": {
-          "uri": "data/7381e3e08a3fe229fa516fc0abf20950_7_0.hic",
+          "uri": "data/f329aa022d2aa8aea5316bfa9c7cc113_8_0.hic",
           "locationType": "UriLocation"
         }
       },
@@ -603,29 +663,29 @@
       "displays": [
         {
           "type": "LinearHicDisplay",
-          "displayId": "7381e3e08a3fe229fa516fc0abf20950_7_0_LinearHicDisplay"
+          "displayId": "f329aa022d2aa8aea5316bfa9c7cc113_8_0_LinearHicDisplay"
         }
       ],
       "metadata": {
-        "dataset_id": "bc183b162fdbb361",
+        "dataset_id": "6294e1cb82136e37",
         "dataset_hid": "11",
         "dataset_size": "931 bytes",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2333\">hic</a>",
         "dataset_file_ext": "hic",
-        "history_id": "ffb0709d52bfbdea",
+        "history_id": "4d30d636fed0a9f6",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/ffb0709d52bfbdea\">Tool Test History for jbrowse2/3.6.5+galaxy0-0</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/4d30d636fed0a9f6\">Tool Test History for jbrowse2/3.6.5+galaxy1-0</a>",
         "metadata_dbkey": "?",
         "metadata_version": "9",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/bc183b162fdbb361/show_params\">upload1</a>"
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/6294e1cb82136e37/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "MafTrack",
-      "trackId": "0448d8682eef9e71183fbc9b84962afa_8_0",
+      "trackId": "74b81aa00dec3d38a9ac2a1176c3cc7e_9_0",
       "name": "merlinlastz.maf",
       "adapter": {
         "type": "MafTabixAdapter",
@@ -639,11 +699,11 @@
           "Merlin6"
         ],
         "bedGzLocation": {
-          "uri": "data/0448d8682eef9e71183fbc9b84962afa_8_0.maf.gz"
+          "uri": "data/74b81aa00dec3d38a9ac2a1176c3cc7e_9_0.maf.gz"
         },
         "index": {
           "location": {
-            "uri": "data/0448d8682eef9e71183fbc9b84962afa_8_0.maf.gz.tbi"
+            "uri": "data/74b81aa00dec3d38a9ac2a1176c3cc7e_9_0.maf.gz.tbi"
           }
         }
       },
@@ -656,33 +716,31 @@
       "displays": [
         {
           "type": "LinearMafDisplay",
-          "displayId": "0448d8682eef9e71183fbc9b84962afa_8_0_LinearMafDisplay"
+          "displayId": "74b81aa00dec3d38a9ac2a1176c3cc7e_9_0_LinearMafDisplay"
         }
       ],
       "metadata": {
-        "dataset_id": "4a7d65b0c4d72bd3",
+        "dataset_id": "7217695b024bd3ec",
         "dataset_hid": "12",
         "dataset_size": "1.5 KB",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_3008\">maf</a>",
         "dataset_file_ext": "maf",
-        "history_id": "ffb0709d52bfbdea",
+        "history_id": "4d30d636fed0a9f6",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/ffb0709d52bfbdea\">Tool Test History for jbrowse2/3.6.5+galaxy0-0</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/4d30d636fed0a9f6\">Tool Test History for jbrowse2/3.6.5+galaxy1-0</a>",
         "metadata_dbkey": "?",
         "metadata_data_lines": "0",
-        "metadata_species": "[\"Merlin\", \"Merlin1\", \"Merlin2\", \"Merlin3\", \"Merlin4\", \"Merlin5\", \"Merlin6\"]",
+        "metadata_species": "Merlin,Merlin1,Merlin2,Merlin3,Merlin4,Merlin5,Merlin6",
         "metadata_blocks": "6",
-        "metadata_species_chromosomes": "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX",
-        "metadata_maf_index": "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/4a7d65b0c4d72bd3/show_params\">upload1</a>"
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/7217695b024bd3ec/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "GCContentTrack",
-      "trackId": "936a5285fbedf1c37f5daf26837035b2_9_0",
+      "trackId": "936a5285fbedf1c37f5daf26837035b2_10_0",
       "name": "GC Content",
       "adapter": {
         "type": "BgzipFastaAdapter",
@@ -708,7 +766,7 @@
       "displays": [
         {
           "type": "LinearGCContentDisplay",
-          "displayId": "936a5285fbedf1c37f5daf26837035b2_9_0_LinearGCContentDisplay"
+          "displayId": "936a5285fbedf1c37f5daf26837035b2_10_0_LinearGCContentDisplay"
         }
       ]
     }
diff -r 93fdd696c281 -r e237edee9a53 test-data/out/01_all_tracks/galaxy.xml
--- a/test-data/out/01_all_tracks/galaxy.xml	Thu Oct 02 10:20:29 2025 +0000
+++ b/test-data/out/01_all_tracks/galaxy.xml	Fri Oct 24 07:50:40 2025 +0000
@@ -12,25 +12,25 @@
         <galaxyUrl>http://localhost:8080</galaxyUrl>
     </metadata>
     <assembly>
-            <genome path="/tmp/tmpgvo11tmf/files/9/2/a/dataset_92aaecec-b349-4c14-bda6-e269d6466611.dat" label="merlin.fa">
+            <genome path="/tmp/tmpiyg6gzbz/files/f/3/c/dataset_f3c0184e-59c4-433e-8dd8-681079b35a97.dat" label="merlin.fa">
             <metadata>
-                <dataset id="ffb0709d52bfbdea" hid="1"
+                <dataset id="4d30d636fed0a9f6" hid="1"
                     size="171.6 KB"
                     edam_format="format_1929"
                     file_ext="fasta"
                     dname = "merlin.fa" />
-                <history id="ffb0709d52bfbdea"
+                <history id="4d30d636fed0a9f6"
                     user_email="planemo@galaxyproject.org"
                     user_id="1"
-                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-0"/>
+                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-0"/>
                 <metadata
                         dbkey="?"
                         data_lines="2881"
                         sequences="1"
                     />
                 <tool
-                    tool_id="upload1"
-                    tool_version="1.1.7"
+                    tool_id="__DATA_FETCH__"
+                    tool_version="0.1.0"
                     />
             </metadata>
             </genome>
@@ -40,28 +40,28 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/3/3/2/dataset_332bfd0e-e9c1-4d46-94e8-e0f9cfd6eeee.dat" ext="gff3" label="merlin.gff">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/6/c/7/dataset_6c7ccdb8-be7f-4998-be93-92e5098e16ae.dat" ext="gff3" label="merlin.gff">
                         <metadata>
-                        <dataset id="33b9ecfea4207697" hid="2"
+                        <dataset id="2a23db38ccbbc7de" hid="2"
                             size="110.3 KB"
                             edam_format="format_1975"
                             file_ext="gff3" />
-                        <history id="ffb0709d52bfbdea"
+                        <history id="4d30d636fed0a9f6"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-0"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-0"/>
                         <metadata
                                 dbkey="?"
                                 data_lines="1228"
                                 comment_lines="2"
                                 columns="9"
-                                column_names="[]"
+                                column_names="__ob____cb__"
                                 delimiter="__tc__"
                                 attributes="4"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
@@ -95,61 +95,118 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/4/5/f/dataset_45fd75ec-a81d-4419-b00b-867540edefb3.dat" ext="bed" label="test-3.bed">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/d/c/f/dataset_dcf75edc-7a03-4e95-b28c-47ae364af589.dat" ext="gtf" label="merlin.gtf">
                         <metadata>
-                        <dataset id="dad64ae4d71c7372" hid="3"
+                        <dataset id="0b7812b25f4cfb76" hid="3"
+                            size="25.0 KB"
+                            edam_format="format_2306"
+                            file_ext="gtf" />
+                        <history id="4d30d636fed0a9f6"
+                            user_email="planemo@galaxyproject.org"
+                            user_id="1"
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-0"/>
+                        <metadata
+                                dbkey="?"
+                                data_lines="292"
+                                comment_lines="0"
+                                columns="9"
+                                column_names="__ob____cb__"
+                                delimiter="__tc__"
+                                attributes="2"
+                            />
+                        <tool
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
+                            />
+                        </metadata>
+                    </trackFile>
+                    </files>
+
+            <options>
+                <style>
+                        <display>LinearBasicDisplay</display>
+
+                            <show_labels type="boolean">true</show_labels>
+                            <show_descriptions type="boolean">true</show_descriptions>
+                            <labels_name>jexl:get(feature,'name') || get(feature,'id')</labels_name>
+                            <descriptions_name>jexl:get(feature,'note') || get(feature,'description')</descriptions_name>
+                            <display_mode>normal</display_mode>
+                            <max_height type="integer">600</max_height>
+
+
+                </style>
+
+                    <formatdetails>
+                        <depth>1</depth>
+                    </formatdetails>
+
+
+                    <gff>
+                    <index>false</index>
+                    </gff>
+            </options>
+        </track>
+        <track cat="Default" format="gene_calls" visibility="default_on">
+
+
+                    <files>
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/c/3/e/dataset_c3ee5cf0-0cb6-4585-a7d6-d5ddcded7371.dat" ext="bed" label="test-3.bed">
+                        <metadata>
+                        <dataset id="bd91a97d652fafe1" hid="4"
                             size="49 bytes"
                             edam_format="format_3003"
                             file_ext="bed" />
-                        <history id="ffb0709d52bfbdea"
+                        <history id="4d30d636fed0a9f6"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-0"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-0"/>
                         <metadata
                                 dbkey="?"
                                 data_lines="3"
                                 comment_lines="0"
                                 columns="3"
-                                column_names="[]"
+                                column_names="__ob____cb__"
                                 delimiter="__tc__"
                                 chromCol="1"
                                 startCol="2"
                                 endCol="3"
                                 strandCol="0"
-                                viz_filter_cols="[4]"
+                                nameCol="0"
+                                viz_filter_cols="4"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/8/3/9/dataset_839210d9-cf81-49bb-b733-f14be084f8aa.dat" ext="bed" label="test-6.bed">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/7/2/0/dataset_72051c30-7fb8-4063-af07-c74536915fa9.dat" ext="bed" label="test-6.bed">
                         <metadata>
-                        <dataset id="36cc4ad69bb5f2a1" hid="4"
+                        <dataset id="3aa468ce9e79eed2" hid="5"
                             size="180 bytes"
                             edam_format="format_3003"
                             file_ext="bed" />
-                        <history id="ffb0709d52bfbdea"
+                        <history id="4d30d636fed0a9f6"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-0"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-0"/>
                         <metadata
                                 dbkey="?"
                                 data_lines="3"
                                 comment_lines="0"
                                 columns="6"
-                                column_names="[]"
+                                column_names="__ob____cb__"
                                 delimiter="__tc__"
                                 chromCol="1"
                                 startCol="2"
                                 endCol="3"
                                 strandCol="6"
-                                viz_filter_cols="[4]"
+                                nameCol="4"
+                                viz_filter_cols="4"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
@@ -183,31 +240,30 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/f/0/2/dataset_f0263ec1-34ec-43b3-871b-39d6e44f8703.dat" ext="bam" label="merlin-sample.bam">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/8/a/5/dataset_8a5eca75-b2e7-436a-8596-659ca480cfc2.dat" ext="bam" label="merlin-sample.bam">
                         <metadata>
-                        <dataset id="ea3d8239d386c6a4" hid="5"
+                        <dataset id="c8d274edba5d366b" hid="6"
                             size="12.9 KB"
                             edam_format="format_2572"
                             file_ext="bam" />
-                        <history id="ffb0709d52bfbdea"
+                        <history id="4d30d636fed0a9f6"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-0"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-0"/>
                         <metadata
                                 dbkey="?"
                                 columns="12"
-                                column_names="[&quot;QNAME&quot;, &quot;FLAG&quot;, &quot;RNAME&quot;, &quot;POS&quot;, &quot;MAPQ&quot;, &quot;CIGAR&quot;, &quot;MRNM&quot;, &quot;MPOS&quot;, &quot;ISIZE&quot;, &quot;SEQ&quot;, &quot;QUAL&quot;, &quot;OPT&quot;]"
+                                column_names="__ob____sq__QNAME__sq__, __sq__FLAG__sq__, __sq__RNAME__sq__, __sq__POS__sq__, __sq__MAPQ__sq__, __sq__CIGAR__sq__, __sq__MRNM__sq__, __sq__MPOS__sq__, __sq__ISIZE__sq__, __sq__SEQ__sq__, __sq__QUAL__sq__, __sq__OPT__sq____cb__"
                                 bam_version="1.3"
                                 sort_order="coordinate"
-                                read_groups="[]"
-                                reference_names="[&quot;Merlin&quot;]"
-                                reference_lengths="[172788]"
-                                bam_header="{&quot;HD&quot;: {&quot;SO&quot;: &quot;coordinate&quot;, &quot;VN&quot;: &quot;1.3&quot;}, &quot;PG&quot;: [{&quot;CL&quot;: &quot;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&quot;, &quot;ID&quot;: &quot;minimap2&quot;, &quot;PN&quot;: &quot;minimap2&quot;, &quot;VN&quot;: &quot;2.5-r572&quot;}], &quot;SQ&quot;: [{&quot;LN&quot;: 172788, &quot;SN&quot;: &quot;Merlin&quot;}]}"
-                                bam_index="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
+                                read_groups="__ob____cb__"
+                                reference_names="__ob____sq__Merlin__sq____cb__"
+                                reference_lengths="__ob__172788__cb__"
+                                bam_header="__oc____sq__HD__sq__: __oc____sq__SO__sq__: __sq__coordinate__sq__, __sq__VN__sq__: __sq__1.3__sq____cc__, __sq__PG__sq__: __ob____oc____sq__CL__sq__: __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__, __sq__ID__sq__: __sq__minimap2__sq__, __sq__PN__sq__: __sq__minimap2__sq__, __sq__VN__sq__: __sq__2.5-r572__sq____cc____cb__, __sq__SQ__sq__: __ob____oc____sq__LN__sq__: 172788, __sq__SN__sq__: __sq__Merlin__sq____cc____cb____cc__"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
@@ -225,7 +281,7 @@
 
                     <pileup>
                             <bam_indices>
-                                    <bam_index>/tmp/tmpgvo11tmf/files/_metadata_files/f/b/d/metadata_fbd6b6b1-16cf-4eb2-b415-ed9608b99203.dat</bam_index>
+                                    <bam_index>/tmp/tmpiyg6gzbz/files/_metadata_files/2/1/b/metadata_21b9af11-e7ea-4393-ba2a-b79f92ff130c.dat</bam_index>
                             </bam_indices>
                     </pileup>
             </options>
@@ -234,22 +290,22 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/4/c/b/dataset_4cb5c8f6-fe5d-4ea0-bdc7-8d5a462676f8.dat" ext="bigwig" label="data.bw">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/7/8/e/dataset_78e8146d-3719-46af-acda-41f5a2678a26.dat" ext="bigwig" label="data.bw">
                         <metadata>
-                        <dataset id="d753b8dba6e25d09" hid="8"
+                        <dataset id="2f8b42de958784ae" hid="7"
                             size="81.6 KB"
                             edam_format="format_3006"
                             file_ext="bigwig" />
-                        <history id="ffb0709d52bfbdea"
+                        <history id="4d30d636fed0a9f6"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-0"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-0"/>
                         <metadata
                                 dbkey="?"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
@@ -274,24 +330,23 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/0/2/d/dataset_02df8cff-9b5e-4548-8087-12b66cb989e1.dat" ext="cram" label="merlin-sample.cram">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/f/0/7/dataset_f07f766a-6f31-4207-85c3-0c86ff22b574.dat" ext="cram" label="merlin-sample.cram">
                         <metadata>
-                        <dataset id="1f72eafab720ae62" hid="7"
+                        <dataset id="76ca3a0a3de24f95" hid="8"
                             size="8.3 KB"
                             edam_format="format_3462"
                             file_ext="cram" />
-                        <history id="ffb0709d52bfbdea"
+                        <history id="4d30d636fed0a9f6"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-0"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-0"/>
                         <metadata
                                 dbkey="?"
                                 cram_version="3.0"
-                                cram_index="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
@@ -309,7 +364,7 @@
 
                     <cram>
                             <cram_indices>
-                                <cram_index>/tmp/tmpgvo11tmf/files/_metadata_files/8/b/b/metadata_8bb20c68-09a9-49f2-9281-f376d48cfc30.dat</cram_index>
+                                <cram_index>/tmp/tmpiyg6gzbz/files/_metadata_files/5/7/3/metadata_5734b699-7e5d-438c-bd25-c2736b084db4.dat</cram_index>
                             </cram_indices>
                     </cram>
             </options>
@@ -318,41 +373,41 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/4/c/b/dataset_4cb5c8f6-fe5d-4ea0-bdc7-8d5a462676f8.dat" ext="bigwig" label="data.bw">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/7/8/e/dataset_78e8146d-3719-46af-acda-41f5a2678a26.dat" ext="bigwig" label="data.bw">
                         <metadata>
-                        <dataset id="d753b8dba6e25d09" hid="8"
+                        <dataset id="2f8b42de958784ae" hid="7"
                             size="81.6 KB"
                             edam_format="format_3006"
                             file_ext="bigwig" />
-                        <history id="ffb0709d52bfbdea"
+                        <history id="4d30d636fed0a9f6"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-0"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-0"/>
                         <metadata
                                 dbkey="?"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/1/b/0/dataset_1b015933-e132-43fb-bc26-ee5d1a0b7b9a.dat" ext="bigwig" label="smaller2.bw">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/a/9/3/dataset_a9398956-bf32-43da-8bb1-047d817af62a.dat" ext="bigwig" label="smaller2.bw">
                         <metadata>
-                        <dataset id="ee963fc82e556fe8" hid="9"
+                        <dataset id="fff5871153f6d061" hid="9"
                             size="10.9 KB"
                             edam_format="format_3006"
                             file_ext="bigwig" />
-                        <history id="ffb0709d52bfbdea"
+                        <history id="4d30d636fed0a9f6"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-0"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-0"/>
                         <metadata
                                 dbkey="?"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
@@ -377,29 +432,29 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/6/a/5/dataset_6a574bcf-cc1d-4a8a-b69e-e98bd1617f5e.dat" ext="vcf" label="test.vcf">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/3/e/3/dataset_3e3ea273-7836-480f-a599-c0c8e3878ed7.dat" ext="vcf" label="test.vcf">
                         <metadata>
-                        <dataset id="2a8101cbb778a3ae" hid="10"
+                        <dataset id="d68659e09db1368d" hid="10"
                             size="1.5 KB"
                             edam_format="format_3016"
                             file_ext="vcf" />
-                        <history id="ffb0709d52bfbdea"
+                        <history id="4d30d636fed0a9f6"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-0"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-0"/>
                         <metadata
                                 dbkey="?"
                                 data_lines="5"
                                 comment_lines="18"
                                 columns="12"
-                                column_names="[]"
+                                column_names="__ob____cb__"
                                 delimiter="__tc__"
-                                viz_filter_cols="[5]"
-                                sample_names="[&quot;NA00001&quot;, &quot;NA00002&quot;, &quot;NA00003&quot;]"
+                                viz_filter_cols="5"
+                                sample_names="__ob____sq__NA00001__sq__, __sq__NA00002__sq__, __sq__NA00003__sq____cb__"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
@@ -421,23 +476,23 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/7/2/7/dataset_7278954d-ff52-449f-8bc0-c7400b60b2d5.dat" ext="hic" label="merlin.hic">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/9/e/7/dataset_9e7fc4c4-f84c-436c-95d4-d1f26d102b1e.dat" ext="hic" label="merlin.hic">
                         <metadata>
-                        <dataset id="bc183b162fdbb361" hid="11"
+                        <dataset id="6294e1cb82136e37" hid="11"
                             size="931 bytes"
                             edam_format="format_2333"
                             file_ext="hic" />
-                        <history id="ffb0709d52bfbdea"
+                        <history id="4d30d636fed0a9f6"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-0"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-0"/>
                         <metadata
                                 dbkey="?"
                                 version="9"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
@@ -461,27 +516,25 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/5/e/2/dataset_5e253171-263d-484f-a87f-c6931b8befbb.dat" ext="maf" label="merlinlastz.maf">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/6/d/8/dataset_6d887995-018c-4119-ae61-2bb8af89301f.dat" ext="maf" label="merlinlastz.maf">
                         <metadata>
-                        <dataset id="4a7d65b0c4d72bd3" hid="12"
+                        <dataset id="7217695b024bd3ec" hid="12"
                             size="1.5 KB"
                             edam_format="format_3008"
                             file_ext="maf" />
-                        <history id="ffb0709d52bfbdea"
+                        <history id="4d30d636fed0a9f6"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-0"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-0"/>
                         <metadata
                                 dbkey="?"
                                 data_lines="0"
-                                species="[&quot;Merlin&quot;, &quot;Merlin1&quot;, &quot;Merlin2&quot;, &quot;Merlin3&quot;, &quot;Merlin4&quot;, &quot;Merlin5&quot;, &quot;Merlin6&quot;]"
+                                species="Merlin,Merlin1,Merlin2,Merlin3,Merlin4,Merlin5,Merlin6"
                                 blocks="6"
-                                species_chromosomes="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
-                                maf_index="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
diff -r 93fdd696c281 -r e237edee9a53 test-data/out/03_synteny/config.json
--- a/test-data/out/03_synteny/config.json	Thu Oct 02 10:20:29 2025 +0000
+++ b/test-data/out/03_synteny/config.json	Fri Oct 24 07:50:40 2025 +0000
@@ -118,7 +118,7 @@
               "assembly": "merlin.fa",
               "loc": "Merlin",
               "tracks": [
-                "934c1f5638ce0d620590c14ae0784692_0_0"
+                "82179179689d9c4c5bdef6eec72630d5_0_0"
               ]
             }
           }
@@ -129,11 +129,11 @@
             "tracks": [
               {
                 "type": "SyntenyTrack",
-                "configuration": "561a4df3bf3652f55cb5419b02dba7f2_0_0",
+                "configuration": "2d3285aa6e070d75c8017044c0deaafd_0_0",
                 "displays": [
                   {
                     "type": "LinearSyntenyDisplay",
-                    "configuration": "561a4df3bf3652f55cb5419b02dba7f2_0_0_LinearSyntenyDisplay"
+                    "configuration": "2d3285aa6e070d75c8017044c0deaafd_0_0_LinearSyntenyDisplay"
                   }
                 ]
               }
@@ -146,11 +146,11 @@
             "tracks": [
               {
                 "type": "SyntenyTrack",
-                "configuration": "32a851bec2514d0aae57afbe0ee757bf_0_0",
+                "configuration": "443bf95452978ab205004d18f01b7011_0_0",
                 "displays": [
                   {
                     "type": "LinearSyntenyDisplay",
-                    "configuration": "32a851bec2514d0aae57afbe0ee757bf_0_0_LinearSyntenyDisplay"
+                    "configuration": "443bf95452978ab205004d18f01b7011_0_0_LinearSyntenyDisplay"
                   }
                 ]
               }
@@ -165,12 +165,12 @@
   "tracks": [
     {
       "type": "QuantitativeTrack",
-      "trackId": "934c1f5638ce0d620590c14ae0784692_0_0",
+      "trackId": "82179179689d9c4c5bdef6eec72630d5_0_0",
       "name": "data.bw",
       "adapter": {
         "type": "BigWigAdapter",
         "bigWigLocation": {
-          "uri": "data/934c1f5638ce0d620590c14ae0784692_0_0.bw",
+          "uri": "data/82179179689d9c4c5bdef6eec72630d5_0_0.bw",
           "locationType": "UriLocation"
         }
       },
@@ -183,29 +183,29 @@
       "displays": [
         {
           "type": "LinearWiggleDisplay",
-          "displayId": "934c1f5638ce0d620590c14ae0784692_0_0_LinearWiggleDisplay",
+          "displayId": "82179179689d9c4c5bdef6eec72630d5_0_0_LinearWiggleDisplay",
           "defaultRendering": "xyplot"
         }
       ],
       "metadata": {
-        "dataset_id": "bbbd1a67b59f937f",
+        "dataset_id": "7a9728aeed7a3efa",
         "dataset_hid": "6",
         "dataset_size": "81.6 KB",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_3006\">bigwig</a>",
         "dataset_file_ext": "bigwig",
-        "history_id": "dad64ae4d71c7372",
+        "history_id": "0b7812b25f4cfb76",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/dad64ae4d71c7372\">Tool Test History for jbrowse2/3.6.5+galaxy0-2</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/0b7812b25f4cfb76\">Tool Test History for jbrowse2/3.6.5+galaxy1-2</a>",
         "metadata_dbkey": "?",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/bbbd1a67b59f937f/show_params\">upload1</a>"
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/7a9728aeed7a3efa/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "SyntenyTrack",
-      "trackId": "561a4df3bf3652f55cb5419b02dba7f2_0_0",
+      "trackId": "2d3285aa6e070d75c8017044c0deaafd_0_0",
       "name": "merlun_on_merlon.paf",
       "adapter": {
         "assemblyNames": [
@@ -214,11 +214,11 @@
         ],
         "type": "PairwiseIndexedPAFAdapter",
         "pifGzLocation": {
-          "uri": "data/561a4df3bf3652f55cb5419b02dba7f2_0_0.pif.gz"
+          "uri": "data/2d3285aa6e070d75c8017044c0deaafd_0_0.pif.gz"
         },
         "index": {
           "location": {
-            "uri": "data/561a4df3bf3652f55cb5419b02dba7f2_0_0.pif.gz.tbi"
+            "uri": "data/2d3285aa6e070d75c8017044c0deaafd_0_0.pif.gz.tbi"
           }
         }
       },
@@ -232,29 +232,29 @@
       "displays": [
         {
           "type": "LinearSyntenyDisplay",
-          "displayId": "561a4df3bf3652f55cb5419b02dba7f2_0_0_LinearSyntenyDisplay"
+          "displayId": "2d3285aa6e070d75c8017044c0deaafd_0_0_LinearSyntenyDisplay"
         }
       ],
       "metadata": {
-        "dataset_id": "890f38a71ba6ec9e",
+        "dataset_id": "e744a972b308a2d0",
         "dataset_hid": "2",
         "dataset_size": "227 bytes",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2330\">paf</a>",
         "dataset_file_ext": "paf",
-        "history_id": "dad64ae4d71c7372",
+        "history_id": "0b7812b25f4cfb76",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/dad64ae4d71c7372\">Tool Test History for jbrowse2/3.6.5+galaxy0-2</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/0b7812b25f4cfb76\">Tool Test History for jbrowse2/3.6.5+galaxy1-2</a>",
         "metadata_dbkey": "?",
         "metadata_data_lines": "2",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/890f38a71ba6ec9e/show_params\">upload1</a>"
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/e744a972b308a2d0/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "SyntenyTrack",
-      "trackId": "32a851bec2514d0aae57afbe0ee757bf_0_0",
+      "trackId": "443bf95452978ab205004d18f01b7011_0_0",
       "name": "merlon_on_merlin.paf",
       "adapter": {
         "assemblyNames": [
@@ -263,11 +263,11 @@
         ],
         "type": "PairwiseIndexedPAFAdapter",
         "pifGzLocation": {
-          "uri": "data/32a851bec2514d0aae57afbe0ee757bf_0_0.pif.gz"
+          "uri": "data/443bf95452978ab205004d18f01b7011_0_0.pif.gz"
         },
         "index": {
           "location": {
-            "uri": "data/32a851bec2514d0aae57afbe0ee757bf_0_0.pif.gz.tbi"
+            "uri": "data/443bf95452978ab205004d18f01b7011_0_0.pif.gz.tbi"
           }
         }
       },
@@ -281,24 +281,24 @@
       "displays": [
         {
           "type": "LinearSyntenyDisplay",
-          "displayId": "32a851bec2514d0aae57afbe0ee757bf_0_0_LinearSyntenyDisplay"
+          "displayId": "443bf95452978ab205004d18f01b7011_0_0_LinearSyntenyDisplay"
         }
       ],
       "metadata": {
-        "dataset_id": "fbad2d6a8ae62498",
+        "dataset_id": "1f8c95c7204ee5b9",
         "dataset_hid": "4",
         "dataset_size": "127 bytes",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2330\">paf</a>",
         "dataset_file_ext": "paf",
-        "history_id": "dad64ae4d71c7372",
+        "history_id": "0b7812b25f4cfb76",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/dad64ae4d71c7372\">Tool Test History for jbrowse2/3.6.5+galaxy0-2</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/0b7812b25f4cfb76\">Tool Test History for jbrowse2/3.6.5+galaxy1-2</a>",
         "metadata_dbkey": "?",
         "metadata_data_lines": "1",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/fbad2d6a8ae62498/show_params\">upload1</a>"
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/1f8c95c7204ee5b9/show_params\">__DATA_FETCH__</a>"
       }
     }
   ],
diff -r 93fdd696c281 -r e237edee9a53 test-data/out/03_synteny/galaxy.xml
--- a/test-data/out/03_synteny/galaxy.xml	Thu Oct 02 10:20:29 2025 +0000
+++ b/test-data/out/03_synteny/galaxy.xml	Fri Oct 24 07:50:40 2025 +0000
@@ -12,51 +12,51 @@
         <galaxyUrl>http://localhost:8080</galaxyUrl>
     </metadata>
     <assembly>
-            <genome path="/tmp/tmpgvo11tmf/files/8/f/0/dataset_8f0d6595-a68d-4be0-8ac7-61dfd1088596.dat" label="merlun.fa">
+            <genome path="/tmp/tmpiyg6gzbz/files/e/f/e/dataset_efe9082c-0a47-4f29-b471-263f76881e43.dat" label="merlun.fa">
             <metadata>
-                <dataset id="faee5844a632ee94" hid="1"
+                <dataset id="42ed1747fda63c08" hid="1"
                     size="158.8 KB"
                     edam_format="format_1929"
                     file_ext="fasta"
                     dname = "merlun.fa" />
-                <history id="dad64ae4d71c7372"
+                <history id="0b7812b25f4cfb76"
                     user_email="planemo@galaxyproject.org"
                     user_id="1"
-                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-2"/>
+                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-2"/>
                 <metadata
                         dbkey="?"
                         data_lines="2666"
                         sequences="1"
                     />
                 <tool
-                    tool_id="upload1"
-                    tool_version="1.1.7"
+                    tool_id="__DATA_FETCH__"
+                    tool_version="0.1.0"
                     />
             </metadata>
             </genome>
         <defaultLocation></defaultLocation>
     <tracks>
-        <track cat="Default" format="synteny" visibility="default_off">
+        <track cat="Default" format="synteny" visibility="default_on">
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/4/f/4/dataset_4f4bc28d-2919-4545-8017-f4b4132ef764.dat" ext="paf" label="merlun_on_merlon.paf">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/5/8/c/dataset_58ca4b5e-c634-4686-86f5-8697451aef9b.dat" ext="paf" label="merlun_on_merlon.paf">
                         <metadata>
-                        <dataset id="890f38a71ba6ec9e" hid="2"
+                        <dataset id="e744a972b308a2d0" hid="2"
                             size="227 bytes"
                             edam_format="format_2330"
                             file_ext="paf" />
-                        <history id="dad64ae4d71c7372"
+                        <history id="0b7812b25f4cfb76"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-2"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-2"/>
                         <metadata
                                 dbkey="?"
                                 data_lines="2"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
@@ -79,51 +79,51 @@
     </tracks>
     </assembly>
     <assembly>
-            <genome path="/tmp/tmpgvo11tmf/files/c/1/7/dataset_c17ecf0a-592f-4e02-915f-28968c7204e4.dat" label="merlon.fa">
+            <genome path="/tmp/tmpiyg6gzbz/files/7/6/6/dataset_76654e69-cc8c-4461-8f92-ea2d9a7fa9c8.dat" label="merlon.fa">
             <metadata>
-                <dataset id="e1770ae07453b348" hid="3"
+                <dataset id="1755c1ca08cd39a9" hid="3"
                     size="155.3 KB"
                     edam_format="format_1929"
                     file_ext="fasta"
                     dname = "merlon.fa" />
-                <history id="dad64ae4d71c7372"
+                <history id="0b7812b25f4cfb76"
                     user_email="planemo@galaxyproject.org"
                     user_id="1"
-                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-2"/>
+                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-2"/>
                 <metadata
                         dbkey="?"
                         data_lines="2608"
                         sequences="1"
                     />
                 <tool
-                    tool_id="upload1"
-                    tool_version="1.1.7"
+                    tool_id="__DATA_FETCH__"
+                    tool_version="0.1.0"
                     />
             </metadata>
             </genome>
         <defaultLocation></defaultLocation>
     <tracks>
-        <track cat="Default" format="synteny" visibility="default_off">
+        <track cat="Default" format="synteny" visibility="default_on">
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/c/b/f/dataset_cbf9364c-3c39-46a5-bb7f-cc8bdbdc1267.dat" ext="paf" label="merlon_on_merlin.paf">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/b/2/0/dataset_b20f1b4c-528e-4b33-9f76-3158ecf3e64a.dat" ext="paf" label="merlon_on_merlin.paf">
                         <metadata>
-                        <dataset id="fbad2d6a8ae62498" hid="4"
+                        <dataset id="1f8c95c7204ee5b9" hid="4"
                             size="127 bytes"
                             edam_format="format_2330"
                             file_ext="paf" />
-                        <history id="dad64ae4d71c7372"
+                        <history id="0b7812b25f4cfb76"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-2"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-2"/>
                         <metadata
                                 dbkey="?"
                                 data_lines="1"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
@@ -146,25 +146,25 @@
     </tracks>
     </assembly>
     <assembly>
-            <genome path="/tmp/tmpgvo11tmf/files/3/8/c/dataset_38c183ee-4de2-4b8a-a3bc-2e31912083fa.dat" label="merlin.fa">
+            <genome path="/tmp/tmpiyg6gzbz/files/a/6/7/dataset_a67ee65b-0f84-4ad9-8984-3dc0baf46d35.dat" label="merlin.fa">
             <metadata>
-                <dataset id="915adfc032ee90e6" hid="5"
+                <dataset id="30deb7a376313549" hid="5"
                     size="171.6 KB"
                     edam_format="format_1929"
                     file_ext="fasta"
                     dname = "merlin.fa" />
-                <history id="dad64ae4d71c7372"
+                <history id="0b7812b25f4cfb76"
                     user_email="planemo@galaxyproject.org"
                     user_id="1"
-                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-2"/>
+                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-2"/>
                 <metadata
                         dbkey="?"
                         data_lines="2881"
                         sequences="1"
                     />
                 <tool
-                    tool_id="upload1"
-                    tool_version="1.1.7"
+                    tool_id="__DATA_FETCH__"
+                    tool_version="0.1.0"
                     />
             </metadata>
             </genome>
@@ -174,22 +174,22 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/3/2/6/dataset_3264bccf-57cd-4c47-ad23-d1c3c781da07.dat" ext="bigwig" label="data.bw">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/8/5/9/dataset_85947fa0-916f-4366-8386-4681c41b6405.dat" ext="bigwig" label="data.bw">
                         <metadata>
-                        <dataset id="bbbd1a67b59f937f" hid="6"
+                        <dataset id="7a9728aeed7a3efa" hid="6"
                             size="81.6 KB"
                             edam_format="format_3006"
                             file_ext="bigwig" />
-                        <history id="dad64ae4d71c7372"
+                        <history id="0b7812b25f4cfb76"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-2"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-2"/>
                         <metadata
                                 dbkey="?"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
diff -r 93fdd696c281 -r e237edee9a53 test-data/out/04_synteny_remote/config.json
--- a/test-data/out/04_synteny_remote/config.json	Thu Oct 02 10:20:29 2025 +0000
+++ b/test-data/out/04_synteny_remote/config.json	Fri Oct 24 07:50:40 2025 +0000
@@ -97,11 +97,11 @@
             "tracks": [
               {
                 "type": "SyntenyTrack",
-                "configuration": "0530135e064b54c99df62def400c3292_0_0",
+                "configuration": "80ba0000256d270f3eed70e2de2e9458_0_0",
                 "displays": [
                   {
                     "type": "LinearSyntenyDisplay",
-                    "configuration": "0530135e064b54c99df62def400c3292_0_0_LinearSyntenyDisplay"
+                    "configuration": "80ba0000256d270f3eed70e2de2e9458_0_0_LinearSyntenyDisplay"
                   }
                 ]
               }
@@ -116,7 +116,7 @@
   "tracks": [
     {
       "type": "SyntenyTrack",
-      "trackId": "0530135e064b54c99df62def400c3292_0_0",
+      "trackId": "80ba0000256d270f3eed70e2de2e9458_0_0",
       "name": "peach-grape-map.paf",
       "adapter": {
         "assemblyNames": [
@@ -125,11 +125,11 @@
         ],
         "type": "PairwiseIndexedPAFAdapter",
         "pifGzLocation": {
-          "uri": "data/0530135e064b54c99df62def400c3292_0_0.pif.gz"
+          "uri": "data/80ba0000256d270f3eed70e2de2e9458_0_0.pif.gz"
         },
         "index": {
           "location": {
-            "uri": "data/0530135e064b54c99df62def400c3292_0_0.pif.gz.tbi"
+            "uri": "data/80ba0000256d270f3eed70e2de2e9458_0_0.pif.gz.tbi"
           }
         }
       },
@@ -143,24 +143,24 @@
       "displays": [
         {
           "type": "LinearSyntenyDisplay",
-          "displayId": "0530135e064b54c99df62def400c3292_0_0_LinearSyntenyDisplay"
+          "displayId": "80ba0000256d270f3eed70e2de2e9458_0_0_LinearSyntenyDisplay"
         }
       ],
       "metadata": {
-        "dataset_id": "49124efef65eb81f",
+        "dataset_id": "5e7c5784e865b42d",
         "dataset_hid": "1",
         "dataset_size": "238.1 KB",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2330\">paf</a>",
         "dataset_file_ext": "paf",
-        "history_id": "36cc4ad69bb5f2a1",
+        "history_id": "bd91a97d652fafe1",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/36cc4ad69bb5f2a1\">Tool Test History for jbrowse2/3.6.5+galaxy0-3</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/bd91a97d652fafe1\">Tool Test History for jbrowse2/3.6.5+galaxy1-3</a>",
         "metadata_dbkey": "?",
         "metadata_data_lines": "1911",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/49124efef65eb81f/show_params\">upload1</a>"
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/5e7c5784e865b42d/show_params\">__DATA_FETCH__</a>"
       }
     }
   ],
diff -r 93fdd696c281 -r e237edee9a53 test-data/out/04_synteny_remote/galaxy.xml
--- a/test-data/out/04_synteny_remote/galaxy.xml	Thu Oct 02 10:20:29 2025 +0000
+++ b/test-data/out/04_synteny_remote/galaxy.xml	Fri Oct 24 07:50:40 2025 +0000
@@ -17,27 +17,27 @@
             </genome>
         <defaultLocation></defaultLocation>
     <tracks>
-        <track cat="Default" format="synteny" visibility="default_off">
+        <track cat="Default" format="synteny" visibility="default_on">
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/a/1/f/dataset_a1f11daf-86d1-489f-a779-7e18e6f10a9f.dat" ext="paf" label="peach-grape-map.paf">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/8/a/a/dataset_8aac4d06-9a9b-4d73-b231-2864581b0dfa.dat" ext="paf" label="peach-grape-map.paf">
                         <metadata>
-                        <dataset id="49124efef65eb81f" hid="1"
+                        <dataset id="5e7c5784e865b42d" hid="1"
                             size="238.1 KB"
                             edam_format="format_2330"
                             file_ext="paf" />
-                        <history id="36cc4ad69bb5f2a1"
+                        <history id="bd91a97d652fafe1"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-3"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-3"/>
                         <metadata
                                 dbkey="?"
                                 data_lines="1911"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
diff -r 93fdd696c281 -r e237edee9a53 test-data/out/05_synteny_full_remote/galaxy.xml
--- a/test-data/out/05_synteny_full_remote/galaxy.xml	Thu Oct 02 10:20:29 2025 +0000
+++ b/test-data/out/05_synteny_full_remote/galaxy.xml	Fri Oct 24 07:50:40 2025 +0000
@@ -17,7 +17,7 @@
             </genome>
         <defaultLocation></defaultLocation>
     <tracks>
-        <track cat="Default" format="synteny" visibility="default_off">
+        <track cat="Default" format="synteny" visibility="default_on">
 
 
                     <files>
diff -r 93fdd696c281 -r e237edee9a53 test-data/out/06_various_options/config.json
--- a/test-data/out/06_various_options/config.json	Thu Oct 02 10:20:29 2025 +0000
+++ b/test-data/out/06_various_options/config.json	Fri Oct 24 07:50:40 2025 +0000
@@ -72,7 +72,7 @@
           "assembly": "merlin.fa",
           "loc": "Merlin:1000-2000",
           "tracks": [
-            "1d4288426ee65828142bd0ec1611ca5a_0_0"
+            "9164da821dd9f40efa61a737d8dbd031_0_0"
           ]
         }
       }
@@ -81,17 +81,17 @@
   "tracks": [
     {
       "type": "FeatureTrack",
-      "trackId": "1d4288426ee65828142bd0ec1611ca5a_0_0",
+      "trackId": "9164da821dd9f40efa61a737d8dbd031_0_0",
       "name": "merlin.gff",
       "adapter": {
         "type": "Gff3TabixAdapter",
         "gffGzLocation": {
-          "uri": "data/1d4288426ee65828142bd0ec1611ca5a_0_0.gff.gz",
+          "uri": "data/9164da821dd9f40efa61a737d8dbd031_0_0.gff.gz",
           "locationType": "UriLocation"
         },
         "index": {
           "location": {
-            "uri": "data/1d4288426ee65828142bd0ec1611ca5a_0_0.gff.gz.tbi",
+            "uri": "data/9164da821dd9f40efa61a737d8dbd031_0_0.gff.gz.tbi",
             "locationType": "UriLocation"
           },
           "indexType": "TBI"
@@ -106,7 +106,7 @@
       "displays": [
         {
           "type": "LinearBasicDisplay",
-          "displayId": "1d4288426ee65828142bd0ec1611ca5a_0_0_LinearBasicDisplay",
+          "displayId": "9164da821dd9f40efa61a737d8dbd031_0_0_LinearBasicDisplay",
           "renderer": {
             "type": "SvgFeatureRenderer",
             "showLabels": true,
@@ -133,17 +133,17 @@
     },
     {
       "type": "FeatureTrack",
-      "trackId": "3ab3c20156596dd17db795bdda1f7c1a_1_0",
+      "trackId": "b26da96d1d07207823e585f65ca15149_1_0",
       "name": "1.gff",
       "adapter": {
         "type": "Gff3TabixAdapter",
         "gffGzLocation": {
-          "uri": "data/3ab3c20156596dd17db795bdda1f7c1a_1_0.gff.gz",
+          "uri": "data/b26da96d1d07207823e585f65ca15149_1_0.gff.gz",
           "locationType": "UriLocation"
         },
         "index": {
           "location": {
-            "uri": "data/3ab3c20156596dd17db795bdda1f7c1a_1_0.gff.gz.tbi",
+            "uri": "data/b26da96d1d07207823e585f65ca15149_1_0.gff.gz.tbi",
             "locationType": "UriLocation"
           },
           "indexType": "TBI"
@@ -158,7 +158,7 @@
       "displays": [
         {
           "type": "LinearArcDisplay",
-          "displayId": "3ab3c20156596dd17db795bdda1f7c1a_1_0_LinearArcDisplay",
+          "displayId": "b26da96d1d07207823e585f65ca15149_1_0_LinearArcDisplay",
           "renderer": {
             "type": "ArcRenderer",
             "label": "jexl:get(feature,'score')",
@@ -170,25 +170,25 @@
         "depth": 1
       },
       "metadata": {
-        "dataset_id": "f4d493e76c714bd7",
+        "dataset_id": "8d08779b916d2c74",
         "dataset_hid": "6",
         "dataset_size": "2.3 KB",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_1975\">gff3</a>",
         "dataset_file_ext": "gff3",
-        "history_id": "052ea72eccff1e52",
+        "history_id": "c8d274edba5d366b",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/052ea72eccff1e52\">Tool Test History for jbrowse2/3.6.5+galaxy0-5</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/c8d274edba5d366b\">Tool Test History for jbrowse2/3.6.5+galaxy1-5</a>",
         "metadata_dbkey": "?",
         "metadata_data_lines": "27",
         "metadata_comment_lines": "19",
         "metadata_columns": "9",
         "metadata_column_names": "[]",
-        "metadata_delimiter": "__tc__",
+        "metadata_delimiter": "\t",
         "metadata_attributes": "6",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/f4d493e76c714bd7/show_params\">upload1</a>"
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/8d08779b916d2c74/show_params\">__DATA_FETCH__</a>"
       }
     }
   ],
@@ -214,4 +214,4 @@
       ]
     }
   ]
-}
+}
\ No newline at end of file
diff -r 93fdd696c281 -r e237edee9a53 test-data/out/06_various_options/galaxy.xml
--- a/test-data/out/06_various_options/galaxy.xml	Thu Oct 02 10:20:29 2025 +0000
+++ b/test-data/out/06_various_options/galaxy.xml	Fri Oct 24 07:50:40 2025 +0000
@@ -12,29 +12,29 @@
         <galaxyUrl>http://localhost:8080</galaxyUrl>
     </metadata>
     <assembly>
-            <genome path="/tmp/tmpgvo11tmf/files/c/2/a/dataset_c2a24553-0ee6-41cb-9183-50cd34872b77.dat" label="merlin.fa">
+            <genome path="/tmp/tmpiyg6gzbz/files/5/2/9/dataset_5296eab5-9843-40c5-9db9-4aa93249c833.dat" label="merlin.fa">
             <metadata>
-                <dataset id="c400d50a71327edf" hid="1"
+                <dataset id="09545c40d817e546" hid="1"
                     size="171.6 KB"
                     edam_format="format_1929"
                     file_ext="fasta"
                     dname = "merlin.fa" />
-                <history id="052ea72eccff1e52"
+                <history id="c8d274edba5d366b"
                     user_email="planemo@galaxyproject.org"
                     user_id="1"
-                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-5"/>
+                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-5"/>
                 <metadata
                         dbkey="?"
                         data_lines="2881"
                         sequences="1"
                     />
                 <tool
-                    tool_id="upload1"
-                    tool_version="1.1.7"
+                    tool_id="__DATA_FETCH__"
+                    tool_version="0.1.0"
                     />
             </metadata>
-                <ref_name_aliases path="/tmp/tmpgvo11tmf/files/b/5/c/dataset_b5c38813-a540-4237-ab54-9ae57f46d215.dat" />
-                <cytobands path="/tmp/tmpgvo11tmf/files/a/3/f/dataset_a3f516d2-9465-4fdb-9dbb-0f678ff96599.dat" />
+                <ref_name_aliases path="/tmp/tmpiyg6gzbz/files/1/1/5/dataset_1151e202-f9f3-4110-b64f-333acec46e55.dat" />
+                <cytobands path="/tmp/tmpiyg6gzbz/files/d/3/5/dataset_d3500267-21d7-4211-b238-9f11ef1a0e95.dat" />
             </genome>
         <defaultLocation>Merlin:1000..2000</defaultLocation>
     <tracks>
@@ -42,9 +42,9 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/7/c/8/dataset_7c87c268-43bb-4c4f-83e0-ea613fa25543.dat" ext="gff3" label="merlin.gff">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/2/3/b/dataset_23b6b090-77a2-4dca-afb1-45c1f639ca3f.dat" ext="gff3" label="merlin.gff">
                         <metadata>
-                            <bonus src="/tmp/tmpgvo11tmf/files/c/2/6/dataset_c267020e-a497-4cf4-b448-7c66892d627b.dat" />
+                            <bonus src="/tmp/tmpiyg6gzbz/files/8/a/a/dataset_8aa7709d-337e-4620-b838-7c4ea7cabf2f.dat" />
                         </metadata>
                     </trackFile>
                     </files>
@@ -79,28 +79,28 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmpgvo11tmf/files/8/7/b/dataset_87bd0e2d-5796-4db5-8d0f-5654c2b26710.dat" ext="gff3" label="1.gff">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/a/9/e/dataset_a9e599f6-9e07-4ca5-9574-a46f79d83567.dat" ext="gff3" label="1.gff">
                         <metadata>
-                        <dataset id="f4d493e76c714bd7" hid="6"
+                        <dataset id="8d08779b916d2c74" hid="6"
                             size="2.3 KB"
                             edam_format="format_1975"
                             file_ext="gff3" />
-                        <history id="052ea72eccff1e52"
+                        <history id="c8d274edba5d366b"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-5"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-5"/>
                         <metadata
                                 dbkey="?"
                                 data_lines="27"
                                 comment_lines="19"
                                 columns="9"
-                                column_names="[]"
+                                column_names="__ob____cb__"
                                 delimiter="__tc__"
                                 attributes="6"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
diff -r 93fdd696c281 -r e237edee9a53 test-data/out/07_synteny_mixed/config.json
--- a/test-data/out/07_synteny_mixed/config.json	Thu Oct 02 10:20:29 2025 +0000
+++ b/test-data/out/07_synteny_mixed/config.json	Fri Oct 24 07:50:40 2025 +0000
@@ -102,8 +102,7 @@
               "assembly": "merlun.fa",
               "loc": "Merlun",
               "tracks": [
-                "17f324230d6997928e1eca50228bd09d_0_0",
-                "17f324230d6997928e1eca50228bd09d_1_0"
+                "f27027d9cba656ee7279114b4764a1a9_1_0"
               ]
             }
           },
@@ -113,8 +112,7 @@
               "assembly": "merlon.fa",
               "loc": "Merlon",
               "tracks": [
-                "33429c271bc47d6279b48d1eaaf4d1e8_0_0",
-                "33429c271bc47d6279b48d1eaaf4d1e8_1_0"
+                "9ab20cffedd38e60ca92f0454b9745db_1_0"
               ]
             }
           },
@@ -124,28 +122,63 @@
               "assembly": "merlin.fa",
               "loc": "Merlin",
               "tracks": [
-                "9353a848a5e1df8b38605dbc140d95dd_0_0"
+                "40c5d3cdfaa1318fd0d68918cd144f36_0_0"
               ]
             }
           }
         ],
-        "levels": []
+        "levels": [
+          {
+            "type": "LinearSyntenyViewHelper",
+            "tracks": [
+              {
+                "type": "SyntenyTrack",
+                "configuration": "f27027d9cba656ee7279114b4764a1a9_0_0",
+                "displays": [
+                  {
+                    "type": "LinearSyntenyDisplay",
+                    "configuration": "f27027d9cba656ee7279114b4764a1a9_0_0_LinearSyntenyDisplay"
+                  }
+                ]
+              }
+            ],
+            "height": 100,
+            "level": 0
+          },
+          {
+            "type": "LinearSyntenyViewHelper",
+            "tracks": [
+              {
+                "type": "SyntenyTrack",
+                "configuration": "9ab20cffedd38e60ca92f0454b9745db_0_0",
+                "displays": [
+                  {
+                    "type": "LinearSyntenyDisplay",
+                    "configuration": "9ab20cffedd38e60ca92f0454b9745db_0_0_LinearSyntenyDisplay"
+                  }
+                ]
+              }
+            ],
+            "height": 100,
+            "level": 1
+          }
+        ]
       }
     ]
   },
   "tracks": [
     {
       "type": "SyntenyTrack",
-      "trackId": "17f324230d6997928e1eca50228bd09d_0_0",
+      "trackId": "f27027d9cba656ee7279114b4764a1a9_1_0",
       "name": "merlun_on_merlon.paf",
       "adapter": {
         "type": "PairwiseIndexedPAFAdapter",
         "pifGzLocation": {
-          "uri": "data/17f324230d6997928e1eca50228bd09d_0_0.pif.gz"
+          "uri": "data/f27027d9cba656ee7279114b4764a1a9_1_0.pif.gz"
         },
         "index": {
           "location": {
-            "uri": "data/17f324230d6997928e1eca50228bd09d_0_0.pif.gz.tbi"
+            "uri": "data/f27027d9cba656ee7279114b4764a1a9_1_0.pif.gz.tbi"
           }
         }
       },
@@ -158,62 +191,7 @@
       "displays": [
         {
           "type": "LinearBasicDisplay",
-          "displayId": "17f324230d6997928e1eca50228bd09d_0_0_LinearBasicDisplay",
-          "renderer": {
-            "type": "SvgFeatureRenderer",
-            "showLabels": true,
-            "showDescriptions": true,
-            "labels": {
-              "name": "jexl:get(feature,'name') || get(feature,'id')",
-              "description": "jexl:get(feature,'note') || get(feature,'description')"
-            },
-            "displayMode": "normal",
-            "maxHeight": 1200
-          }
-        }
-      ],
-      "metadata": {
-        "dataset_id": "2ca7380062475cc2",
-        "dataset_hid": "2",
-        "dataset_size": "227 bytes",
-        "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2330\">paf</a>",
-        "dataset_file_ext": "paf",
-        "history_id": "fa950b0ef319061e",
-        "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
-        "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/fa950b0ef319061e\">Tool Test History for jbrowse2/3.6.5+galaxy0-6</a>",
-        "metadata_dbkey": "?",
-        "metadata_data_lines": "2",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/2ca7380062475cc2/show_params\">upload1</a>"
-      }
-    },
-    {
-      "type": "SyntenyTrack",
-      "trackId": "17f324230d6997928e1eca50228bd09d_1_0",
-      "name": "merlun_on_merlon.paf",
-      "adapter": {
-        "type": "PairwiseIndexedPAFAdapter",
-        "pifGzLocation": {
-          "uri": "data/17f324230d6997928e1eca50228bd09d_1_0.pif.gz"
-        },
-        "index": {
-          "location": {
-            "uri": "data/17f324230d6997928e1eca50228bd09d_1_0.pif.gz.tbi"
-          }
-        }
-      },
-      "category": [
-        "Default"
-      ],
-      "assemblyNames": [
-        "merlun.fa"
-      ],
-      "displays": [
-        {
-          "type": "LinearBasicDisplay",
-          "displayId": "17f324230d6997928e1eca50228bd09d_1_0_LinearBasicDisplay",
+          "displayId": "f27027d9cba656ee7279114b4764a1a9_1_0_LinearBasicDisplay",
           "renderer": {
             "type": "SvgFeatureRenderer",
             "showLabels": true,
@@ -228,34 +206,34 @@
         }
       ],
       "metadata": {
-        "dataset_id": "2ca7380062475cc2",
+        "dataset_id": "0193a46a40878ddb",
         "dataset_hid": "2",
         "dataset_size": "227 bytes",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2330\">paf</a>",
         "dataset_file_ext": "paf",
-        "history_id": "fa950b0ef319061e",
+        "history_id": "2f8b42de958784ae",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/fa950b0ef319061e\">Tool Test History for jbrowse2/3.6.5+galaxy0-6</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/2f8b42de958784ae\">Tool Test History for jbrowse2/3.6.5+galaxy1-6</a>",
         "metadata_dbkey": "?",
         "metadata_data_lines": "2",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/2ca7380062475cc2/show_params\">upload1</a>"
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/0193a46a40878ddb/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "SyntenyTrack",
-      "trackId": "33429c271bc47d6279b48d1eaaf4d1e8_0_0",
+      "trackId": "9ab20cffedd38e60ca92f0454b9745db_1_0",
       "name": "merlon_on_merlin.paf",
       "adapter": {
         "type": "PairwiseIndexedPAFAdapter",
         "pifGzLocation": {
-          "uri": "data/33429c271bc47d6279b48d1eaaf4d1e8_0_0.pif.gz"
+          "uri": "data/9ab20cffedd38e60ca92f0454b9745db_1_0.pif.gz"
         },
         "index": {
           "location": {
-            "uri": "data/33429c271bc47d6279b48d1eaaf4d1e8_0_0.pif.gz.tbi"
+            "uri": "data/9ab20cffedd38e60ca92f0454b9745db_1_0.pif.gz.tbi"
           }
         }
       },
@@ -268,7 +246,7 @@
       "displays": [
         {
           "type": "LinearBasicDisplay",
-          "displayId": "33429c271bc47d6279b48d1eaaf4d1e8_0_0_LinearBasicDisplay",
+          "displayId": "9ab20cffedd38e60ca92f0454b9745db_1_0_LinearBasicDisplay",
           "renderer": {
             "type": "SvgFeatureRenderer",
             "showLabels": true,
@@ -283,85 +261,30 @@
         }
       ],
       "metadata": {
-        "dataset_id": "6f8f1ec4766df755",
+        "dataset_id": "4b6ef6ca3df7dc79",
         "dataset_hid": "4",
         "dataset_size": "127 bytes",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2330\">paf</a>",
         "dataset_file_ext": "paf",
-        "history_id": "fa950b0ef319061e",
+        "history_id": "2f8b42de958784ae",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/fa950b0ef319061e\">Tool Test History for jbrowse2/3.6.5+galaxy0-6</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/2f8b42de958784ae\">Tool Test History for jbrowse2/3.6.5+galaxy1-6</a>",
         "metadata_dbkey": "?",
         "metadata_data_lines": "1",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/6f8f1ec4766df755/show_params\">upload1</a>"
-      }
-    },
-    {
-      "type": "SyntenyTrack",
-      "trackId": "33429c271bc47d6279b48d1eaaf4d1e8_1_0",
-      "name": "merlon_on_merlin.paf",
-      "adapter": {
-        "type": "PairwiseIndexedPAFAdapter",
-        "pifGzLocation": {
-          "uri": "data/33429c271bc47d6279b48d1eaaf4d1e8_1_0.pif.gz"
-        },
-        "index": {
-          "location": {
-            "uri": "data/33429c271bc47d6279b48d1eaaf4d1e8_1_0.pif.gz.tbi"
-          }
-        }
-      },
-      "category": [
-        "Default"
-      ],
-      "assemblyNames": [
-        "merlon.fa"
-      ],
-      "displays": [
-        {
-          "type": "LinearBasicDisplay",
-          "displayId": "33429c271bc47d6279b48d1eaaf4d1e8_1_0_LinearBasicDisplay",
-          "renderer": {
-            "type": "SvgFeatureRenderer",
-            "showLabels": true,
-            "showDescriptions": true,
-            "labels": {
-              "name": "jexl:get(feature,'name') || get(feature,'id')",
-              "description": "jexl:get(feature,'note') || get(feature,'description')"
-            },
-            "displayMode": "normal",
-            "maxHeight": 1200
-          }
-        }
-      ],
-      "metadata": {
-        "dataset_id": "6f8f1ec4766df755",
-        "dataset_hid": "4",
-        "dataset_size": "127 bytes",
-        "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2330\">paf</a>",
-        "dataset_file_ext": "paf",
-        "history_id": "fa950b0ef319061e",
-        "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
-        "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/fa950b0ef319061e\">Tool Test History for jbrowse2/3.6.5+galaxy0-6</a>",
-        "metadata_dbkey": "?",
-        "metadata_data_lines": "1",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/6f8f1ec4766df755/show_params\">upload1</a>"
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/4b6ef6ca3df7dc79/show_params\">__DATA_FETCH__</a>"
       }
     },
     {
       "type": "QuantitativeTrack",
-      "trackId": "9353a848a5e1df8b38605dbc140d95dd_0_0",
+      "trackId": "40c5d3cdfaa1318fd0d68918cd144f36_0_0",
       "name": "data.bw",
       "adapter": {
         "type": "BigWigAdapter",
         "bigWigLocation": {
-          "uri": "data/9353a848a5e1df8b38605dbc140d95dd_0_0.bw",
+          "uri": "data/40c5d3cdfaa1318fd0d68918cd144f36_0_0.bw",
           "locationType": "UriLocation"
         }
       },
@@ -374,24 +297,122 @@
       "displays": [
         {
           "type": "LinearWiggleDisplay",
-          "displayId": "9353a848a5e1df8b38605dbc140d95dd_0_0_LinearWiggleDisplay",
+          "displayId": "40c5d3cdfaa1318fd0d68918cd144f36_0_0_LinearWiggleDisplay",
           "defaultRendering": "xyplot"
         }
       ],
       "metadata": {
-        "dataset_id": "9956239aff51cae9",
+        "dataset_id": "956e46a817a35762",
         "dataset_hid": "6",
         "dataset_size": "81.6 KB",
         "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_3006\">bigwig</a>",
         "dataset_file_ext": "bigwig",
-        "history_id": "fa950b0ef319061e",
+        "history_id": "2f8b42de958784ae",
+        "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
+        "history_user_id": "1",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/2f8b42de958784ae\">Tool Test History for jbrowse2/3.6.5+galaxy1-6</a>",
+        "metadata_dbkey": "?",
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/956e46a817a35762/show_params\">__DATA_FETCH__</a>"
+      }
+    },
+    {
+      "type": "SyntenyTrack",
+      "trackId": "f27027d9cba656ee7279114b4764a1a9_0_0",
+      "name": "merlun_on_merlon.paf",
+      "adapter": {
+        "assemblyNames": [
+          "merlun.fa",
+          "merlon.fa"
+        ],
+        "type": "PairwiseIndexedPAFAdapter",
+        "pifGzLocation": {
+          "uri": "data/f27027d9cba656ee7279114b4764a1a9_0_0.pif.gz"
+        },
+        "index": {
+          "location": {
+            "uri": "data/f27027d9cba656ee7279114b4764a1a9_0_0.pif.gz.tbi"
+          }
+        }
+      },
+      "category": [
+        "Default"
+      ],
+      "assemblyNames": [
+        "merlun.fa",
+        "merlon.fa"
+      ],
+      "displays": [
+        {
+          "type": "LinearSyntenyDisplay",
+          "displayId": "f27027d9cba656ee7279114b4764a1a9_0_0_LinearSyntenyDisplay"
+        }
+      ],
+      "metadata": {
+        "dataset_id": "0193a46a40878ddb",
+        "dataset_hid": "2",
+        "dataset_size": "227 bytes",
+        "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2330\">paf</a>",
+        "dataset_file_ext": "paf",
+        "history_id": "2f8b42de958784ae",
         "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
         "history_user_id": "1",
-        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/fa950b0ef319061e\">Tool Test History for jbrowse2/3.6.5+galaxy0-6</a>",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/2f8b42de958784ae\">Tool Test History for jbrowse2/3.6.5+galaxy1-6</a>",
         "metadata_dbkey": "?",
-        "tool_tool_id": "upload1",
-        "tool_tool_version": "1.1.7",
-        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/9956239aff51cae9/show_params\">upload1</a>"
+        "metadata_data_lines": "2",
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/0193a46a40878ddb/show_params\">__DATA_FETCH__</a>"
+      }
+    },
+    {
+      "type": "SyntenyTrack",
+      "trackId": "9ab20cffedd38e60ca92f0454b9745db_0_0",
+      "name": "merlon_on_merlin.paf",
+      "adapter": {
+        "assemblyNames": [
+          "merlon.fa",
+          "merlin.fa"
+        ],
+        "type": "PairwiseIndexedPAFAdapter",
+        "pifGzLocation": {
+          "uri": "data/9ab20cffedd38e60ca92f0454b9745db_0_0.pif.gz"
+        },
+        "index": {
+          "location": {
+            "uri": "data/9ab20cffedd38e60ca92f0454b9745db_0_0.pif.gz.tbi"
+          }
+        }
+      },
+      "category": [
+        "Default"
+      ],
+      "assemblyNames": [
+        "merlon.fa",
+        "merlin.fa"
+      ],
+      "displays": [
+        {
+          "type": "LinearSyntenyDisplay",
+          "displayId": "9ab20cffedd38e60ca92f0454b9745db_0_0_LinearSyntenyDisplay"
+        }
+      ],
+      "metadata": {
+        "dataset_id": "4b6ef6ca3df7dc79",
+        "dataset_hid": "4",
+        "dataset_size": "127 bytes",
+        "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2330\">paf</a>",
+        "dataset_file_ext": "paf",
+        "history_id": "2f8b42de958784ae",
+        "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
+        "history_user_id": "1",
+        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/2f8b42de958784ae\">Tool Test History for jbrowse2/3.6.5+galaxy1-6</a>",
+        "metadata_dbkey": "?",
+        "metadata_data_lines": "1",
+        "tool_tool_id": "__DATA_FETCH__",
+        "tool_tool_version": "0.1.0",
+        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/4b6ef6ca3df7dc79/show_params\">__DATA_FETCH__</a>"
       }
     }
   ],
diff -r 93fdd696c281 -r e237edee9a53 test-data/out/07_synteny_mixed/galaxy.xml
--- a/test-data/out/07_synteny_mixed/galaxy.xml	Thu Oct 02 10:20:29 2025 +0000
+++ b/test-data/out/07_synteny_mixed/galaxy.xml	Fri Oct 24 07:50:40 2025 +0000
@@ -12,25 +12,25 @@
         <galaxyUrl>http://localhost:8080</galaxyUrl>
     </metadata>
     <assembly>
-            <genome path="/tmp/tmp6b1mtu54/files/6/0/2/dataset_602d83e7-6ec8-4476-a27b-800b4c8d3570.dat" label="merlun.fa">
+            <genome path="/tmp/tmpiyg6gzbz/files/c/c/d/dataset_ccdaa782-b710-408d-b2f0-485e98d73d0c.dat" label="merlun.fa">
             <metadata>
-                <dataset id="ef8367bbbd7a8a28" hid="1"
+                <dataset id="db035faa70b52d68" hid="1"
                     size="158.8 KB"
                     edam_format="format_1929"
                     file_ext="fasta"
                     dname = "merlun.fa" />
-                <history id="fa950b0ef319061e"
+                <history id="2f8b42de958784ae"
                     user_email="planemo@galaxyproject.org"
                     user_id="1"
-                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-6"/>
+                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-6"/>
                 <metadata
                         dbkey="?"
                         data_lines="2666"
                         sequences="1"
                     />
                 <tool
-                    tool_id="upload1"
-                    tool_version="1.1.7"
+                    tool_id="__DATA_FETCH__"
+                    tool_version="0.1.0"
                     />
             </metadata>
             </genome>
@@ -40,23 +40,23 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmp6b1mtu54/files/d/7/0/dataset_d7026439-5ae9-4bc5-8f58-bfe069f89440.dat" ext="paf" label="merlun_on_merlon.paf">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/9/c/c/dataset_9cc8d8bd-cfa4-46bf-ae31-cf6eab61a297.dat" ext="paf" label="merlun_on_merlon.paf">
                         <metadata>
-                        <dataset id="2ca7380062475cc2" hid="2"
+                        <dataset id="0193a46a40878ddb" hid="2"
                             size="227 bytes"
                             edam_format="format_2330"
                             file_ext="paf" />
-                        <history id="fa950b0ef319061e"
+                        <history id="2f8b42de958784ae"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-6"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-6"/>
                         <metadata
                                 dbkey="?"
                                 data_lines="2"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
@@ -64,7 +64,7 @@
 
             <options>
                 <style>
-                        <display>LinearBasicDisplay</display>
+                        <display>LinearSyntenyDisplay</display>
 
 
 
@@ -80,23 +80,23 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmp6b1mtu54/files/d/7/0/dataset_d7026439-5ae9-4bc5-8f58-bfe069f89440.dat" ext="paf" label="merlun_on_merlon.paf">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/9/c/c/dataset_9cc8d8bd-cfa4-46bf-ae31-cf6eab61a297.dat" ext="paf" label="merlun_on_merlon.paf">
                         <metadata>
-                        <dataset id="2ca7380062475cc2" hid="2"
+                        <dataset id="0193a46a40878ddb" hid="2"
                             size="227 bytes"
                             edam_format="format_2330"
                             file_ext="paf" />
-                        <history id="fa950b0ef319061e"
+                        <history id="2f8b42de958784ae"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-6"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-6"/>
                         <metadata
                                 dbkey="?"
                                 data_lines="2"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
@@ -119,25 +119,25 @@
     </tracks>
     </assembly>
     <assembly>
-            <genome path="/tmp/tmp6b1mtu54/files/4/1/2/dataset_412b6a75-3c70-4e00-a139-accf25cb2ea2.dat" label="merlon.fa">
+            <genome path="/tmp/tmpiyg6gzbz/files/a/2/3/dataset_a23e3ae0-cf0b-427c-a8fb-c9a7a93ba5e3.dat" label="merlon.fa">
             <metadata>
-                <dataset id="3c4f82138bb2487a" hid="3"
+                <dataset id="4fedddb5f0b604f3" hid="3"
                     size="155.3 KB"
                     edam_format="format_1929"
                     file_ext="fasta"
                     dname = "merlon.fa" />
-                <history id="fa950b0ef319061e"
+                <history id="2f8b42de958784ae"
                     user_email="planemo@galaxyproject.org"
                     user_id="1"
-                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-6"/>
+                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-6"/>
                 <metadata
                         dbkey="?"
                         data_lines="2608"
                         sequences="1"
                     />
                 <tool
-                    tool_id="upload1"
-                    tool_version="1.1.7"
+                    tool_id="__DATA_FETCH__"
+                    tool_version="0.1.0"
                     />
             </metadata>
             </genome>
@@ -147,23 +147,23 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmp6b1mtu54/files/a/2/8/dataset_a28858a6-9df4-43ad-802c-77a9917bff5d.dat" ext="paf" label="merlon_on_merlin.paf">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/2/1/d/dataset_21dce734-5668-47ae-bdee-4b924bcea3c3.dat" ext="paf" label="merlon_on_merlin.paf">
                         <metadata>
-                        <dataset id="6f8f1ec4766df755" hid="4"
+                        <dataset id="4b6ef6ca3df7dc79" hid="4"
                             size="127 bytes"
                             edam_format="format_2330"
                             file_ext="paf" />
-                        <history id="fa950b0ef319061e"
+                        <history id="2f8b42de958784ae"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-6"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-6"/>
                         <metadata
                                 dbkey="?"
                                 data_lines="1"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
@@ -171,7 +171,7 @@
 
             <options>
                 <style>
-                        <display>LinearBasicDisplay</display>
+                        <display>LinearSyntenyDisplay</display>
 
 
 
@@ -187,23 +187,23 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmp6b1mtu54/files/a/2/8/dataset_a28858a6-9df4-43ad-802c-77a9917bff5d.dat" ext="paf" label="merlon_on_merlin.paf">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/2/1/d/dataset_21dce734-5668-47ae-bdee-4b924bcea3c3.dat" ext="paf" label="merlon_on_merlin.paf">
                         <metadata>
-                        <dataset id="6f8f1ec4766df755" hid="4"
+                        <dataset id="4b6ef6ca3df7dc79" hid="4"
                             size="127 bytes"
                             edam_format="format_2330"
                             file_ext="paf" />
-                        <history id="fa950b0ef319061e"
+                        <history id="2f8b42de958784ae"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-6"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-6"/>
                         <metadata
                                 dbkey="?"
                                 data_lines="1"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>
@@ -226,25 +226,25 @@
     </tracks>
     </assembly>
     <assembly>
-            <genome path="/tmp/tmp6b1mtu54/files/4/8/c/dataset_48c793d9-04d2-4ff5-aab3-ebc8672a4f74.dat" label="merlin.fa">
+            <genome path="/tmp/tmpiyg6gzbz/files/3/2/c/dataset_32c64057-113d-4f64-b4cc-f4123cbefec6.dat" label="merlin.fa">
             <metadata>
-                <dataset id="ae1bab3408d09c53" hid="5"
+                <dataset id="eb1e31c16c0fe718" hid="5"
                     size="171.6 KB"
                     edam_format="format_1929"
                     file_ext="fasta"
                     dname = "merlin.fa" />
-                <history id="fa950b0ef319061e"
+                <history id="2f8b42de958784ae"
                     user_email="planemo@galaxyproject.org"
                     user_id="1"
-                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-6"/>
+                    display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-6"/>
                 <metadata
                         dbkey="?"
                         data_lines="2881"
                         sequences="1"
                     />
                 <tool
-                    tool_id="upload1"
-                    tool_version="1.1.7"
+                    tool_id="__DATA_FETCH__"
+                    tool_version="0.1.0"
                     />
             </metadata>
             </genome>
@@ -254,22 +254,22 @@
 
 
                     <files>
-                    <trackFile path="/tmp/tmp6b1mtu54/files/b/2/b/dataset_b2b742ee-81c2-43c9-9d8b-577115245111.dat" ext="bigwig" label="data.bw">
+                    <trackFile path="/tmp/tmpiyg6gzbz/files/8/6/a/dataset_86a329ba-72ee-4f3c-9e13-2bf70c513a57.dat" ext="bigwig" label="data.bw">
                         <metadata>
-                        <dataset id="9956239aff51cae9" hid="6"
+                        <dataset id="956e46a817a35762" hid="6"
                             size="81.6 KB"
                             edam_format="format_3006"
                             file_ext="bigwig" />
-                        <history id="fa950b0ef319061e"
+                        <history id="2f8b42de958784ae"
                             user_email="planemo@galaxyproject.org"
                             user_id="1"
-                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy0-6"/>
+                            display_name="Tool Test History for jbrowse2/3.6.5+galaxy1-6"/>
                         <metadata
                                 dbkey="?"
                             />
                         <tool
-                            tool_id="upload1"
-                            tool_version="1.1.7"
+                            tool_id="__DATA_FETCH__"
+                            tool_version="0.1.0"
                             />
                         </metadata>
                     </trackFile>