Mercurial > repos > fubar > jbrowse2
changeset 137:e237edee9a53 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse2 commit 5482aa86f906615d9bddcc32cfbc2d45b24e6345
| author | iuc |
|---|---|
| date | Fri, 24 Oct 2025 07:50:40 +0000 |
| parents | 93fdd696c281 |
| children | |
| files | jbrowse2.py jbrowse2.xml macros.xml test-data/gtf/merlin.gtf test-data/out/01_all_tracks/config.json test-data/out/01_all_tracks/galaxy.xml test-data/out/03_synteny/config.json test-data/out/03_synteny/galaxy.xml test-data/out/04_synteny_remote/config.json test-data/out/04_synteny_remote/galaxy.xml test-data/out/05_synteny_full_remote/galaxy.xml test-data/out/06_various_options/config.json test-data/out/06_various_options/galaxy.xml test-data/out/07_synteny_mixed/config.json test-data/out/07_synteny_mixed/galaxy.xml |
| diffstat | 15 files changed, 1170 insertions(+), 609 deletions(-) [+] |
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--- 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)
--- 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('"', """) ${key}="${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="{"type":"BigWigAdapter","bigWigLocation":{"uri":"https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw","locationType":"UriLocation"}}" /> + <has_json_property_with_value property="adapter" value="{"type":"MultiWiggleAdapter","subadapters":[{"type":"BigWigAdapter","name":"SKBR3 pacbio coverage (NGMLR)","bigWigLocation":{"uri":"https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw","locationType":"UriLocation"}}]}" /> + </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
--- 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"/>
--- /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"; +Merlin merlin transcript 2011 3066 . - . transcript_id "Merlin_4_mRNA"; gene_id "Merlin_4" +Merlin merlin exon 2011 3066 . - . transcript_id "Merlin_4_mRNA"; gene_id "Merlin_4"; +Merlin merlin transcript 3066 4796 . - . transcript_id "Merlin_5_exon"; gene_id "Merlin_5_exon" +Merlin merlin CDS 3066 4796 . - 0 transcript_id "Merlin_5_exon"; +Merlin merlin transcript 3066 4796 . - . transcript_id "Merlin_5_mRNA"; gene_id "Merlin_5" +Merlin merlin exon 3066 4796 . - . transcript_id "Merlin_5_mRNA"; gene_id "Merlin_5"; +Merlin merlin transcript 4793 5317 . - . transcript_id "Merlin_6_exon"; gene_id "Merlin_6_exon" +Merlin merlin CDS 4793 5317 . - 0 transcript_id "Merlin_6_exon"; +Merlin merlin transcript 4793 5317 . - . transcript_id "Merlin_6_mRNA"; gene_id "Merlin_6" +Merlin merlin exon 4793 5317 . - . transcript_id "Merlin_6_mRNA"; gene_id "Merlin_6"; +Merlin merlin transcript 5289 6431 . - . transcript_id "Merlin_7_exon"; gene_id "Merlin_7_exon" +Merlin merlin CDS 5289 6431 . - 0 transcript_id "Merlin_7_exon"; +Merlin merlin transcript 5289 6431 . - . transcript_id "Merlin_7_mRNA"; gene_id "Merlin_7" +Merlin merlin exon 5289 6431 . - . transcript_id "Merlin_7_mRNA"; gene_id "Merlin_7"; +Merlin merlin transcript 6428 7180 . - . transcript_id "Merlin_8_exon"; gene_id "Merlin_8_exon" +Merlin merlin CDS 6428 7180 . - 0 transcript_id "Merlin_8_exon"; +Merlin merlin transcript 6428 7180 . - . transcript_id "Merlin_8_mRNA"; gene_id "Merlin_8" +Merlin merlin exon 6428 7180 . - . transcript_id "Merlin_8_mRNA"; gene_id "Merlin_8"; +Merlin merlin transcript 7228 7857 . + . transcript_id "Merlin_9_exon"; gene_id "Merlin_9_exon" +Merlin merlin CDS 7228 7857 . + 0 transcript_id "Merlin_9_exon"; +Merlin merlin transcript 7228 7857 . + . transcript_id "Merlin_9_mRNA"; gene_id "Merlin_9" +Merlin merlin exon 7228 7857 . + . transcript_id "Merlin_9_mRNA"; gene_id "Merlin_9"; +Merlin merlin transcript 7857 8252 . + . transcript_id "Merlin_10_exon"; gene_id "Merlin_10_exon" +Merlin merlin CDS 7857 8252 . + 0 transcript_id "Merlin_10_exon"; +Merlin merlin transcript 7857 8252 . + . transcript_id "Merlin_10_mRNA"; gene_id "Merlin_10" +Merlin merlin exon 7857 8252 . + . transcript_id "Merlin_10_mRNA"; gene_id "Merlin_10"; +Merlin merlin transcript 8340 8753 . + . transcript_id "Merlin_11_exon"; gene_id "Merlin_11_exon" +Merlin merlin CDS 8340 8753 . + 0 transcript_id "Merlin_11_exon"; +Merlin merlin transcript 8340 8753 . + . transcript_id "Merlin_11_mRNA"; gene_id "Merlin_11" +Merlin merlin exon 8340 8753 . + . transcript_id "Merlin_11_mRNA"; gene_id "Merlin_11"; +Merlin merlin transcript 8787 8951 . + . transcript_id "Merlin_12_exon"; gene_id "Merlin_12_exon" +Merlin merlin CDS 8787 8951 . + 0 transcript_id "Merlin_12_exon"; +Merlin merlin transcript 8787 8951 . + . transcript_id "Merlin_12_mRNA"; gene_id "Merlin_12" +Merlin merlin exon 8787 8951 . + . transcript_id "Merlin_12_mRNA"; gene_id "Merlin_12"; +Merlin merlin transcript 9014 9241 . - . transcript_id "Merlin_13_exon"; gene_id "Merlin_13_exon" +Merlin merlin CDS 9014 9241 . - 0 transcript_id "Merlin_13_exon"; +Merlin merlin transcript 9014 9241 . - . transcript_id "Merlin_13_mRNA"; gene_id "Merlin_13" +Merlin merlin exon 9014 9241 . - . transcript_id "Merlin_13_mRNA"; gene_id "Merlin_13"; +Merlin merlin transcript 9248 10747 . - . transcript_id "Merlin_14_exon"; gene_id "Merlin_14_exon" +Merlin merlin CDS 9248 10747 . - 0 transcript_id "Merlin_14_exon"; +Merlin merlin transcript 9248 10747 . - . transcript_id "Merlin_14_mRNA"; gene_id "Merlin_14" +Merlin merlin exon 9248 10747 . - . transcript_id "Merlin_14_mRNA"; gene_id "Merlin_14"; +Merlin merlin transcript 10800 11435 . + . transcript_id "Merlin_15_exon"; gene_id "Merlin_15_exon" +Merlin merlin CDS 10800 11435 . + 0 transcript_id "Merlin_15_exon"; +Merlin merlin transcript 10800 11435 . + . transcript_id "Merlin_15_mRNA"; gene_id "Merlin_15" +Merlin merlin exon 10800 11435 . + . transcript_id "Merlin_15_mRNA"; gene_id "Merlin_15"; +Merlin merlin transcript 11469 12290 . + . transcript_id "Merlin_16_exon"; gene_id "Merlin_16_exon" +Merlin merlin CDS 11469 12290 . + 0 transcript_id "Merlin_16_exon"; +Merlin merlin transcript 11469 12290 . + . transcript_id "Merlin_16_mRNA"; gene_id "Merlin_16" +Merlin merlin exon 11469 12290 . + . transcript_id "Merlin_16_mRNA"; gene_id "Merlin_16"; +Merlin merlin transcript 12365 12601 . + . transcript_id "Merlin_17_exon"; gene_id "Merlin_17_exon" +Merlin merlin CDS 12365 12601 . + 0 transcript_id "Merlin_17_exon"; +Merlin merlin transcript 12365 12601 . + . transcript_id "Merlin_17_mRNA"; gene_id "Merlin_17" +Merlin merlin exon 12365 12601 . + . transcript_id "Merlin_17_mRNA"; gene_id "Merlin_17"; +Merlin merlin transcript 12598 12951 . + . transcript_id "Merlin_18_exon"; gene_id "Merlin_18_exon" +Merlin merlin CDS 12598 12951 . + 0 transcript_id "Merlin_18_exon"; +Merlin merlin transcript 12598 12951 . + . transcript_id "Merlin_18_mRNA"; gene_id "Merlin_18" +Merlin merlin exon 12598 12951 . + . transcript_id "Merlin_18_mRNA"; gene_id "Merlin_18"; +Merlin merlin transcript 13067 13330 . + . transcript_id "Merlin_19_exon"; gene_id "Merlin_19_exon" +Merlin merlin CDS 13067 13330 . + 0 transcript_id "Merlin_19_exon"; +Merlin merlin transcript 13067 13330 . + . transcript_id "Merlin_19_mRNA"; gene_id "Merlin_19" +Merlin merlin exon 13067 13330 . + . transcript_id "Merlin_19_mRNA"; gene_id "Merlin_19"; +Merlin merlin transcript 13340 14341 . + . transcript_id "Merlin_20_exon"; gene_id "Merlin_20_exon" +Merlin merlin CDS 13340 14341 . + 0 transcript_id "Merlin_20_exon"; +Merlin merlin transcript 13340 14341 . + . transcript_id "Merlin_20_mRNA"; gene_id "Merlin_20" +Merlin merlin exon 13340 14341 . + . transcript_id "Merlin_20_mRNA"; gene_id "Merlin_20"; +Merlin merlin transcript 14320 14883 . + . transcript_id "Merlin_21_exon"; gene_id "Merlin_21_exon" +Merlin merlin CDS 14320 14883 . + 0 transcript_id "Merlin_21_exon"; +Merlin merlin transcript 14320 14883 . + . transcript_id "Merlin_21_mRNA"; gene_id "Merlin_21" +Merlin merlin exon 14320 14883 . + . transcript_id "Merlin_21_mRNA"; gene_id "Merlin_21"; +Merlin merlin transcript 14911 16197 . - . transcript_id "Merlin_22_exon"; gene_id "Merlin_22_exon" +Merlin merlin CDS 14911 16197 . - 0 transcript_id "Merlin_22_exon"; +Merlin merlin transcript 14911 16197 . - . transcript_id "Merlin_22_mRNA"; gene_id "Merlin_22" +Merlin merlin exon 14911 16197 . - . transcript_id "Merlin_22_mRNA"; gene_id "Merlin_22"; +Merlin merlin transcript 16289 17836 . - . transcript_id "Merlin_23_exon"; gene_id "Merlin_23_exon" +Merlin merlin CDS 16289 17836 . - 0 transcript_id "Merlin_23_exon"; +Merlin merlin transcript 16289 17836 . - . transcript_id "Merlin_23_mRNA"; gene_id "Merlin_23" +Merlin merlin exon 16289 17836 . - . transcript_id "Merlin_23_mRNA"; gene_id "Merlin_23"; +Merlin merlin transcript 17858 18673 . - . transcript_id "Merlin_24_exon"; gene_id "Merlin_24_exon" +Merlin merlin CDS 17858 18673 . - 0 transcript_id "Merlin_24_exon"; +Merlin merlin transcript 17858 18673 . - . transcript_id "Merlin_24_mRNA"; gene_id "Merlin_24" +Merlin merlin exon 17858 18673 . - . transcript_id "Merlin_24_mRNA"; gene_id "Merlin_24"; +Merlin merlin transcript 18707 19351 . - . transcript_id "Merlin_25_exon"; gene_id "Merlin_25_exon" +Merlin merlin CDS 18707 19351 . - 0 transcript_id "Merlin_25_exon"; +Merlin merlin transcript 18707 19351 . - . transcript_id "Merlin_25_mRNA"; gene_id "Merlin_25" +Merlin merlin exon 18707 19351 . - . transcript_id "Merlin_25_mRNA"; gene_id "Merlin_25"; +Merlin merlin transcript 19351 19776 . - . transcript_id "Merlin_26_exon"; gene_id "Merlin_26_exon" +Merlin merlin CDS 19351 19776 . - 0 transcript_id "Merlin_26_exon"; +Merlin merlin transcript 19351 19776 . - . transcript_id "Merlin_26_mRNA"; gene_id "Merlin_26" +Merlin merlin exon 19351 19776 . - . transcript_id "Merlin_26_mRNA"; gene_id "Merlin_26"; +Merlin merlin transcript 19776 19988 . - . transcript_id "Merlin_27_exon"; gene_id "Merlin_27_exon" +Merlin merlin CDS 19776 19988 . - 0 transcript_id "Merlin_27_exon"; +Merlin merlin transcript 19776 19988 . - . transcript_id "Merlin_27_mRNA"; gene_id "Merlin_27" +Merlin merlin exon 19776 19988 . - . transcript_id "Merlin_27_mRNA"; gene_id "Merlin_27"; +Merlin merlin transcript 19988 21550 . - . transcript_id "Merlin_28_exon"; gene_id "Merlin_28_exon" +Merlin merlin CDS 19988 21550 . - 0 transcript_id "Merlin_28_exon"; +Merlin merlin transcript 19988 21550 . - . transcript_id "Merlin_28_mRNA"; gene_id "Merlin_28" +Merlin merlin exon 19988 21550 . - . transcript_id "Merlin_28_mRNA"; gene_id "Merlin_28"; +Merlin merlin transcript 21625 22116 . - . transcript_id "Merlin_29_exon"; gene_id "Merlin_29_exon" +Merlin merlin CDS 21625 22116 . - 0 transcript_id "Merlin_29_exon"; +Merlin merlin transcript 21625 22116 . - . transcript_id "Merlin_29_mRNA"; gene_id "Merlin_29" +Merlin merlin exon 21625 22116 . - . transcript_id "Merlin_29_mRNA"; gene_id "Merlin_29"; +Merlin merlin transcript 22240 24216 . - . transcript_id "Merlin_30_exon"; gene_id "Merlin_30_exon" +Merlin merlin CDS 22240 24216 . - 0 transcript_id "Merlin_30_exon"; +Merlin merlin transcript 22240 24216 . - . transcript_id "Merlin_30_mRNA"; gene_id "Merlin_30" +Merlin merlin exon 22240 24216 . - . transcript_id "Merlin_30_mRNA"; gene_id "Merlin_30"; +Merlin merlin transcript 24250 26094 . - . transcript_id "Merlin_31_exon"; gene_id "Merlin_31_exon" +Merlin merlin CDS 24250 26094 . - 0 transcript_id "Merlin_31_exon"; +Merlin merlin transcript 24250 26094 . - . transcript_id "Merlin_31_mRNA"; gene_id "Merlin_31" +Merlin merlin exon 24250 26094 . - . transcript_id "Merlin_31_mRNA"; gene_id "Merlin_31"; +Merlin merlin transcript 26072 26569 . - . transcript_id "Merlin_32_exon"; gene_id "Merlin_32_exon" +Merlin merlin CDS 26072 26569 . - 0 transcript_id "Merlin_32_exon"; +Merlin merlin transcript 26072 26569 . - . transcript_id "Merlin_32_mRNA"; gene_id "Merlin_32" +Merlin merlin exon 26072 26569 . - . transcript_id "Merlin_32_mRNA"; gene_id "Merlin_32"; +Merlin merlin transcript 26572 27390 . - . transcript_id "Merlin_33_exon"; gene_id "Merlin_33_exon" +Merlin merlin CDS 26572 27390 . - 0 transcript_id "Merlin_33_exon"; +Merlin merlin transcript 26572 27390 . - . transcript_id "Merlin_33_mRNA"; gene_id "Merlin_33" +Merlin merlin exon 26572 27390 . - . transcript_id "Merlin_33_mRNA"; gene_id "Merlin_33"; +Merlin merlin transcript 27434 28204 . - . transcript_id "Merlin_34_exon"; gene_id "Merlin_34_exon" +Merlin merlin CDS 27434 28204 . - 0 transcript_id "Merlin_34_exon"; +Merlin merlin transcript 27434 28204 . - . transcript_id "Merlin_34_mRNA"; gene_id "Merlin_34" +Merlin merlin exon 27434 28204 . - . transcript_id "Merlin_34_mRNA"; gene_id "Merlin_34"; +Merlin merlin transcript 28201 29130 . - . transcript_id "Merlin_35_exon"; gene_id "Merlin_35_exon" +Merlin merlin CDS 28201 29130 . - 0 transcript_id "Merlin_35_exon"; +Merlin merlin transcript 28201 29130 . - . transcript_id "Merlin_35_mRNA"; gene_id "Merlin_35" +Merlin merlin exon 28201 29130 . - . transcript_id "Merlin_35_mRNA"; gene_id "Merlin_35"; +Merlin merlin transcript 29162 30553 . - . transcript_id "Merlin_36_exon"; gene_id "Merlin_36_exon" +Merlin merlin CDS 29162 30553 . - 0 transcript_id "Merlin_36_exon"; +Merlin merlin transcript 29162 30553 . - . transcript_id "Merlin_36_mRNA"; gene_id "Merlin_36" +Merlin merlin exon 29162 30553 . - . transcript_id "Merlin_36_mRNA"; gene_id "Merlin_36"; +Merlin merlin transcript 30564 31982 . - . transcript_id "Merlin_37_exon"; gene_id "Merlin_37_exon" +Merlin merlin CDS 30564 31982 . - 0 transcript_id "Merlin_37_exon"; +Merlin merlin transcript 30564 31982 . - . transcript_id "Merlin_37_mRNA"; gene_id "Merlin_37" +Merlin merlin exon 30564 31982 . - . transcript_id "Merlin_37_mRNA"; gene_id "Merlin_37"; +Merlin merlin transcript 31982 32632 . - . transcript_id "Merlin_38_exon"; gene_id "Merlin_38_exon" +Merlin merlin CDS 31982 32632 . - 0 transcript_id "Merlin_38_exon"; +Merlin merlin transcript 31982 32632 . - . transcript_id "Merlin_38_mRNA"; gene_id "Merlin_38" +Merlin merlin exon 31982 32632 . - . transcript_id "Merlin_38_mRNA"; gene_id "Merlin_38"; +Merlin merlin transcript 32632 34437 . - . transcript_id "Merlin_39_exon"; gene_id "Merlin_39_exon" +Merlin merlin CDS 32632 34437 . - 0 transcript_id "Merlin_39_exon"; +Merlin merlin transcript 32632 34437 . - . transcript_id "Merlin_39_mRNA"; gene_id "Merlin_39" +Merlin merlin exon 32632 34437 . - . transcript_id "Merlin_39_mRNA"; gene_id "Merlin_39"; +Merlin merlin transcript 34434 35300 . - . transcript_id "Merlin_40_exon"; gene_id "Merlin_40_exon" +Merlin merlin CDS 34434 35300 . - 0 transcript_id "Merlin_40_exon"; +Merlin merlin transcript 34434 35300 . - . transcript_id "Merlin_40_mRNA"; gene_id "Merlin_40" +Merlin merlin exon 34434 35300 . - . transcript_id "Merlin_40_mRNA"; gene_id "Merlin_40"; +Merlin merlin transcript 35372 36385 . - . transcript_id "Merlin_41_exon"; gene_id "Merlin_41_exon" +Merlin merlin CDS 35372 36385 . - 0 transcript_id "Merlin_41_exon"; +Merlin merlin transcript 35372 36385 . - . transcript_id "Merlin_41_mRNA"; gene_id "Merlin_41" +Merlin merlin exon 35372 36385 . - . transcript_id "Merlin_41_mRNA"; gene_id "Merlin_41"; +Merlin merlin transcript 36378 39479 . - . transcript_id "Merlin_42_exon"; gene_id "Merlin_42_exon" +Merlin merlin CDS 36378 39479 . - 0 transcript_id "Merlin_42_exon"; +Merlin merlin transcript 36378 39479 . - . transcript_id "Merlin_42_mRNA"; gene_id "Merlin_42" +Merlin merlin exon 36378 39479 . - . transcript_id "Merlin_42_mRNA"; gene_id "Merlin_42"; +Merlin merlin transcript 39476 41416 . - . transcript_id "Merlin_43_exon"; gene_id "Merlin_43_exon" +Merlin merlin CDS 39476 41416 . - 0 transcript_id "Merlin_43_exon"; +Merlin merlin transcript 39476 41416 . - . transcript_id "Merlin_43_mRNA"; gene_id "Merlin_43" +Merlin merlin exon 39476 41416 . - . transcript_id "Merlin_43_mRNA"; gene_id "Merlin_43"; +Merlin merlin transcript 41416 41709 . - . transcript_id "Merlin_44_exon"; gene_id "Merlin_44_exon" +Merlin merlin CDS 41416 41709 . - 0 transcript_id "Merlin_44_exon"; +Merlin merlin transcript 41416 41709 . - . transcript_id "Merlin_44_mRNA"; gene_id "Merlin_44" +Merlin merlin exon 41416 41709 . - . transcript_id "Merlin_44_mRNA"; gene_id "Merlin_44"; +Merlin merlin transcript 41709 42224 . - . transcript_id "Merlin_45_exon"; gene_id "Merlin_45_exon" +Merlin merlin CDS 41709 42224 . - 0 transcript_id "Merlin_45_exon"; +Merlin merlin transcript 41709 42224 . - . transcript_id "Merlin_45_mRNA"; gene_id "Merlin_45" +Merlin merlin exon 41709 42224 . - . transcript_id "Merlin_45_mRNA"; gene_id "Merlin_45"; +Merlin merlin transcript 42224 43951 . - . transcript_id "Merlin_46_exon"; gene_id "Merlin_46_exon" +Merlin merlin CDS 42224 43951 . - 0 transcript_id "Merlin_46_exon"; +Merlin merlin transcript 42224 43951 . - . transcript_id "Merlin_46_mRNA"; gene_id "Merlin_46" +Merlin merlin exon 42224 43951 . - . transcript_id "Merlin_46_mRNA"; gene_id "Merlin_46"; +Merlin merlin transcript 43951 44526 . - . transcript_id "Merlin_47_exon"; gene_id "Merlin_47_exon" +Merlin merlin CDS 43951 44526 . - 0 transcript_id "Merlin_47_exon"; +Merlin merlin transcript 43951 44526 . - . transcript_id "Merlin_47_mRNA"; gene_id "Merlin_47" +Merlin merlin exon 43951 44526 . - . transcript_id "Merlin_47_mRNA"; gene_id "Merlin_47"; +Merlin merlin transcript 44576 45025 . + . transcript_id "Merlin_48_exon"; gene_id "Merlin_48_exon" +Merlin merlin CDS 44576 45025 . + 0 transcript_id "Merlin_48_exon"; +Merlin merlin transcript 44576 45025 . + . transcript_id "Merlin_48_mRNA"; gene_id "Merlin_48" +Merlin merlin exon 44576 45025 . + . transcript_id "Merlin_48_mRNA"; gene_id "Merlin_48"; +Merlin merlin transcript 45025 45855 . + . transcript_id "Merlin_49_exon"; gene_id "Merlin_49_exon" +Merlin merlin CDS 45025 45855 . + 0 transcript_id "Merlin_49_exon"; +Merlin merlin transcript 45025 45855 . + . transcript_id "Merlin_49_mRNA"; gene_id "Merlin_49" +Merlin merlin exon 45025 45855 . + . transcript_id "Merlin_49_mRNA"; gene_id "Merlin_49"; +Merlin merlin transcript 45940 46527 . + . transcript_id "Merlin_50_exon"; gene_id "Merlin_50_exon" +Merlin merlin CDS 45940 46527 . + 0 transcript_id "Merlin_50_exon"; +Merlin merlin transcript 45940 46527 . + . transcript_id "Merlin_50_mRNA"; gene_id "Merlin_50" +Merlin merlin exon 45940 46527 . + . transcript_id "Merlin_50_mRNA"; gene_id "Merlin_50"; +Merlin merlin transcript 46527 47255 . + . transcript_id "Merlin_51_exon"; gene_id "Merlin_51_exon" +Merlin merlin CDS 46527 47255 . + 0 transcript_id "Merlin_51_exon"; +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";
--- 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" } ] }
--- 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="["QNAME", "FLAG", "RNAME", "POS", "MAPQ", "CIGAR", "MRNM", "MPOS", "ISIZE", "SEQ", "QUAL", "OPT"]" + 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="["Merlin"]" - reference_lengths="[172788]" - 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"}]}" - 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="["NA00001", "NA00002", "NA00003"]" + 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="["Merlin", "Merlin1", "Merlin2", "Merlin3", "Merlin4", "Merlin5", "Merlin6"]" + 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>
--- 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>" } } ],
--- 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>
--- 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>" } } ],
--- 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>
--- 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>
--- 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
--- 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>
--- 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>" } } ],
--- 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>