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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
author bgruening
date Wed, 05 Jun 2024 08:15:49 +0000
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-1:000000000000 0:53c2be00bb6f
1 <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
2 <description>genome browser</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edamInc"/>
7 <xrefs>
8 <xref type="bio.tools">jbrowse2</xref>
9 </xrefs>
10 <expand macro="requirements"/>
11 <required_files>
12 <include path="autogenJB2.py"/>
13 <include path="blastxml_to_gapped_gff3.py"/>
14 <include path="convertMAF.sh"/>
15 <include path="gff3_rebase.py"/>
16 <include path="jb2_webserver.py"/>
17 <include path="jbrowse2.py"/>
18 <include path="maf2bed.py"/>
19 </required_files>
20 <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command>
21 <command detect_errors="aggressive"><![CDATA[
22 mkdir -p '$output.files_path' &&
23 cp '$trackxml' '$output.files_path/galaxy.xml' &&
24 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
25 #if $jbgen.ucol.formcoll=="collect":
26 python '$__tool_directory__/autogenJB2.py'
27 #for $key in $autoCollection.keys():
28 #if $autoCollection[$key].is_collection:
29 #set subCol=$autoCollection[$key]
30 #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf']
31 #if len($pafs) > 0:
32 --pafmeta '$pafs[0]'
33 #set refs = [($pafs[0][2],$subCol[x],x) for x in $subCol.keys() if $subCol[x].ext == 'fasta']
34 #for $ref in $refs:
35 --pafreferencemeta '$ref'
36 #end for
37 #end if
38 #else if $autoCollection[$key].ext == 'fasta':
39 --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
40 #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf']
41 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
42 #else if $autoCollection[$key].ext in ['bam',]
43 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index'
44 #else if $autoCollection[$key].ext in ['cram',]
45 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index'
46 #end if
47 #end for
48 --outdir '$output.files_path'
49 --jbrowse2path \${JBROWSE2_PATH}
50 --sessName "Autogen JBrowse" &&
51 #if $jbgen.zipOut == "true":
52 cd '$output.files_path' &&
53 zip -r - . > '$output'
54 #else
55 cp '$output.files_path/index.html' '$output'
56 #end if
57 #else:
58 python '$__tool_directory__/jbrowse2.py'
59 --jbrowse2path \${JBROWSE2_PATH}
60 --outdir '$output.files_path'
61 --xml '$trackxml' &&
62 #if $jbgen.zipOut == "true":
63 cd '$output.files_path' &&
64 zip -r - . > '$output'
65 #else
66 cp '$output.files_path/index.html' '$output'
67 #end if
68 #end if
69 ]]></command>
70 <configfiles>
71 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
72 <root>
73 <metadata>
74 <general>
75 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
76 <zipOut>${jbgen.zipOut}</zipOut>
77 <analytics>${jbgen.enableAnalytics}</analytics>
78 <primary_color>${jbgen.primary_color}</primary_color>
79 <secondary_color>${jbgen.secondary_color}</secondary_color>
80 <tertiary_color>${jbgen.tertiary_color}</tertiary_color>
81 <quaternary_color>${jbgen.quaternary_color}</quaternary_color>
82 <font_size>${jbgen.font_size}</font_size>
83 <session_name>${jbgen.session_name}</session_name>
84 </general>
85 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
86 </metadata>
87 #if $jbgen.ucol.formcoll=="form":
88 #for $assembly in $assemblies:
89 <assembly>
90 <metadata>
91 <genomes>
92 #if str($assembly.reference_genome.genome_type_select) == "uri":
93 <genome path="${assembly.reference_genome.uri}" label="${assembly.reference_genome.refname}" useuri="yes">
94 <metadata>
95 <dataset
96 dname = "${assembly.reference_genome.refname}" />
97 </metadata>
98 </genome>
99 #else if str($assembly.reference_genome.genome_type_select) == "indexed":
100 <genome path="${assembly.reference_genome.genome.fields.path}" label="${assembly.reference_genome.genome.fields.dbkey}" useuri="no">
101 <metadata>
102 <dataset
103 dname = "${assembly.reference_genome.genome.fields.name}" />
104 </metadata>
105 </genome>
106 #else
107 <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.name}" useuri="no">
108 <metadata>
109
110 <dataset id="${__app__.security.encode_id($assembly.reference_genome.genome.id)}"
111 hid="${assembly.reference_genome.genome.hid}"
112 size="${assembly.reference_genome.genome.get_size(nice_size=True)}"
113 edam_format="${assembly.reference_genome.genome.datatype.edam_format}"
114 file_ext="${assembly.reference_genome.genome.ext}"
115 dname = "${assembly.reference_genome.genome.name}"
116 />
117 <history
118 #if $assembly.reference_genome.genome.history.user:
119 user_email="${assembly.reference_genome.genome.history.user.email}"
120 user_id="${assembly.reference_genome.genome.history.user_id}"
121 display_name="${assembly.reference_genome.genome.history.get_display_name()}"/>
122 #else
123 user_email="anonymous"
124 user_id="-1"
125 display_name="Unnamed History"
126 #end if
127 id="${__app__.security.encode_id($assembly.reference_genome.genome.history_id)}"
128 />
129 <metadata
130 #for (key, value) in $assembly.reference_genome.genome.get_metadata().items():
131 #if "_types" not in $key:
132 #if isinstance($value, list):
133 #set value_str = "[%s]" % ','.join([str(val) for val in value])
134 ${key}="$value_str"
135 #else
136 ${key}="${value}"
137 #end if
138 #end if
139 #end for
140 />
141 <tool
142 tool_id="${assembly.reference_genome.genome.creating_job.tool_id}"
143 tool_version="${assembly.reference_genome.genome.creating_job.tool_version}"
144 />
145 </metadata>
146 </genome>
147 #end if
148 </genomes>
149 </metadata>
150 <tracks>
151 #for $tg in $assembly.track_groups:
152 #for $track in $tg.data_tracks:
153 #set input_exists = "False"
154 #if $track.data_format.useuri.insource == "uri":
155 #if $track.data_format.useuri.annouri:
156 #set input_exists = "True"
157 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
158 <files>
159 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}"
160 label="${track.data_format.useuri.annoname}" useuri="yes">
161 <metadata>
162 <dataset id = "${track.data_format.useuri.annouri}" />
163 </metadata>
164 </trackFile>
165 </files>
166 #end if
167 #else if $track.data_format.useuri.insource == "history":
168 #if $track.data_format.useuri.annotation:
169 #set input_exists = "True"
170 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
171 <files>
172 #for $dataset in $track.data_format.useuri.annotation:
173 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no">
174 <metadata>
175 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
176 size="${dataset.get_size(nice_size=True)}"
177 edam_format="${dataset.datatype.edam_format}"
178 file_ext="${dataset.ext}" />
179 <history id="${__app__.security.encode_id($dataset.history_id)}"
180 #if $dataset.history.user:
181 user_email="${dataset.history.user.email}"
182 user_id="${dataset.history.user_id}"
183 display_name="${dataset.history.get_display_name()}"/>
184 #else
185 user_email="anonymous"
186 user_id="-1"
187 display_name="Unnamed History"/>
188 #end if
189 <metadata
190 #for (key, value) in $dataset.get_metadata().items():
191 #if "_types" not in $key and $value is not None and len(str($value)) < 5000:
192 #if isinstance($value, list):
193 #set value_str = "[%s]" % ','.join([str(val) for val in value])
194 ${key}="$value_str"
195 #else
196 ${key}="${value}"
197 #end if
198 #end if
199 #end for
200 />
201 <tool
202 tool_id="${dataset.creating_job.tool_id}"
203 tool_version="${dataset.creating_job.tool_version}"
204 />
205 </metadata>
206 </trackFile>
207 #end for
208 </files>
209 #end if
210 #end if
211 #if $input_exists == "True":
212 <options>
213 <style>
214 #if str($track.data_format.data_format_select) in ["gff", "bed", "maf", "blastxml"]:
215 <type>${track.data_format.jbstyle.display}</type>
216 #if str($track.data_format.jbstyle.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
217 <trackShowLabels>${track.data_format.jbstyle.show_labels}</trackShowLabels>
218 <trackShowDescriptions>${track.data_format.jbstyle.show_descriptions}</trackShowDescriptions>
219 #end if
220 #else if str($track.data_format.data_format_select) == "vcf":
221 <type>${track.data_format.jbstyle.track_style.display}</type>
222 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
223 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels>
224 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions>
225 #end if
226
227 #end if
228 #if str($track.data_format.data_format_select) in ["bam", "cram"]:
229 <type>LinearAlignmentsDisplay</type>
230 #end if
231 #if str($track.data_format.data_format_select) in ["hic", "cool", "mcool", "scool"]:
232 <type>LinearHicDisplay</type>
233 #end if
234 </style>
235 #if str($track.data_format.data_format_select) == "bam":
236 <bam>
237 <bam_index>
238 #for $dataset in $track.data_format.useuri.annotation:
239 ${dataset} ~ ${dataset.metadata.bam_index},
240 #end for
241 </bam_index>
242 </bam>
243 #else if str($track.data_format.data_format_select) == "cram":
244 <cram>
245 <cram_index>
246 #for $dataset in $track.data_format.useuri.annotation:
247 ${dataset} ~ ${dataset.metadata.cram_index},
248 #end for
249 </cram_index>
250 </cram>
251 #else if str($track.data_format.data_format_select) == "blastxml":
252 <blast>
253 #if str($track.data_format.blast_parent) != "":
254 <parent>${track.data_format.blast_parent}</parent>
255 #end if
256 <protein>${track.data_format.is_protein}</protein>
257 <min_gap>${track.data_format.min_gap}</min_gap>
258 </blast>
259 #else if str($track.data_format.data_format_select) == "gff":
260 <gff>
261 #if $track.data_format.match_part.match_part_select == "true":
262 <match>${track.data_format.match_part.name}</match>
263 #end if
264 </gff>
265 #else if str($track.data_format.data_format_select) == "paf":
266 <paf>
267 #if str($track.data_format.pafuseuri.insource) == "history":
268 <genome>
269 #for $anno in $track.data_format.pafuseuri.annotation:
270 ${anno} ~ ${anno.name},
271 #end for
272 </genome>
273 <useuri>
274 false
275 </useuri>
276 #else:
277 <genome>
278 #for $refgenome in $track.data_format.pafuseuri.refuri:
279 ${refgenome.annotation} ~ ${refgenome.annoname},
280 #end for
281 </genome>
282 <useuri>
283 true
284 </useuri>
285 #end if
286 </paf>
287 #else if str($track.data_format.data_format_select) == "hic":
288 <hic>
289 </hic>
290 #else if str($track.data_format.data_format_select) == "cool":
291 <cool>
292 </cool>
293 #else if str($track.data_format.data_format_select) == "bed":
294 <bed>
295 </bed>
296 #else if str($track.data_format.data_format_select) == "sparql":
297 <label>${track.data_format.label}</label>
298 <sparql>
299 <url>${track.data_format.url}</url>
300 <query>${track.data_format.query}</query>
301 <query_refnames>${track.data_format.query_refnames}</query_refnames>
302 </sparql>
303 #end if
304 </options>
305 </track>
306 #end if
307 #end for
308 #end for
309 </tracks>
310 </assembly>
311 #end for
312 #end if
313 </root>
314 ]]></configfile>
315 </configfiles>
316 <inputs>
317 <repeat name="assemblies" min="1" title="Genome reference to provide display coordinates for this set of tracks" help="JBrowse2 can show a set of tracks for each of multiple genome reference fasta files">
318 <conditional name="reference_genome">
319 <param name="genome_type_select" type="select" label="Reference genome source" help="Select a built in, history or remote tabix URI for the reference track">
320 <option selected="True" value="indexed">Use a Galaxy server built-in genome</option>
321 <option value="history">Use a genome fasta file from the current history</option>
322 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as
323 tabix bgzip with predictable index file URI</option>
324 </param>
325 <when value="indexed">
326 <param name="genome" type="select" optional="true" label="Select a built in reference genome or custom genome" help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome">
327 <options from_data_table="all_fasta">
328 <filter column="2" type="sort_by"/>
329 <validator message="No genomes are available for the selected input dataset" type="no_options"/>
330 </options>
331 </param>
332 </when>
333 <when value="history">
334 <param name="genome" type="data" format="fasta" optional="true" label="Select the reference genome"/>
335 </when>
336 <when value="uri">
337 <param name="uri" type="text" label="URI pointing to tabix compressed fasta"/>
338 <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"/>
339 </when>
340 </conditional>
341 <repeat name="track_groups" title="Track Group">
342 <param name="category" type="text" value="Default" optional="False" label="Track Category" 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."/>
343 <repeat name="data_tracks" title="Annotation Track">
344 <conditional name="data_format" label="Track Data Selection Options">
345 <param name="data_format_select" type="select" label="Track Type">
346 <option value="bam">BAM track. Recommend convert to faster BED unless mapping annotation needed</option>
347 <option value="bed">BED track</option>
348 <option value="bigwig">BigWig track</option>
349 <option value="blastxml">Blast XML track (as GFF3)</option>
350 <option value="cram">CRAM track, we recomment to convert to BED like for BAM</option>
351 <option value="gff">GFF/GFF3 track</option>
352 <option value="cool">HiC as cool/mcool/scool format files</option>
353 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
354 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
355 <option value="paf">PAF - approximate mapping positions between two set of sequences</option>
356 <option value="vcf">VCF SNP track</option>
357 </param>
358 <when value="blastxml">
359 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml"/>
360 <param name="blast_parent" type="data" format="gff3" optional="true" label="Features used in Blast Search" help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."/>
361 <param name="min_gap" type="integer" min="2" value="10" label="Minimum Gap Size" help="before a new match_part feature is created"/>
362 <param name="is_protein" type="boolean" truevalue="true" falsevalue="false" label="Is this a protein blast search?"/>
363 <expand macro="track_styling_vgp"/>
364 <expand macro="track_visibility"/>
365 </when>
366 <when value="vcf">
367 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip"/>
368 <expand macro="track_styling_vcf"/>
369 <expand macro="track_visibility"/>
370 </when>
371 <when value="gff">
372 <expand macro="input_conditional" label="GFF/GFF3 Track Data" format="gff,gff3"/>
373 <conditional name="match_part" label="match/match_part data">
374 <param name="match_part_select" type="select" label="This is match/match_part data" help="Match part data selection ">
375 <option selected="True" value="false">Not match/match part data</option>
376 <option value="true">Match/match part data</option>
377 </param>
378 <when value="true">
379 <param name="name" type="text" value="match" optional="True" label="Match Part Feature Type" help="Match_parts have options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)."/>
380 </when>
381 <when value="false"/>
382 </conditional>
383 <expand macro="track_styling_vgp"/>
384 <expand macro="track_visibility"/>
385 </when>
386 <when value="bam">
387 <expand macro="input_conditional" label="BAM Track Data" format="bam"/>
388 <expand macro="track_visibility"/>
389 </when>
390 <when value="bed">
391 <expand macro="input_conditional" label="BED Track Data" format="bed"/>
392 <expand macro="track_styling_vgp"/>
393 <expand macro="track_visibility"/>
394 </when>
395 <when value="cram">
396 <expand macro="input_conditional" label="CRAM Track Data" format="cram"/>
397 <expand macro="track_visibility"/>
398 </when>
399 <when value="maf">
400 <expand macro="input_conditional" label="MAF Track Data" format="maf"/>
401 <expand macro="track_styling_vgp"/>
402 <expand macro="track_visibility"/>
403 </when>
404 <when value="bigwig">
405 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig"/>
406 <expand macro="track_visibility"/>
407 </when>
408 <when value="paf">
409 <expand macro="input_conditional" label="PAF format synteny mapping data" format="paf" help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references"/>
410 <expand macro="pafref_conditional" label="Comparison genome sequence(s)" format="fasta" help="Paf from these as the reference(s), using the common reference as the reads to map"/>
411 <expand macro="track_visibility"/>
412 </when>
413 <when value="hic">
414 <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic"/>
415 <expand macro="track_visibility"/>
416 </when>
417 <when value="cool">
418 <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool"/>
419 <expand macro="track_visibility"/>
420 </when>
421 </conditional>
422 </repeat>
423 </repeat>
424 </repeat>
425 <expand macro="general_options"/>
426 </inputs>
427 <outputs>
428 <data format="html" name="output" label="JBrowse2: ${jbgen.session_name}">
429 <change_format>
430 <when input="zipOut" value="true" format="zip"/>
431 </change_format>
432 </data>
433 </outputs>
434 <tests>
435 <test>
436 <repeat name="assemblies">
437 <conditional name="reference_genome">
438 <param name="genome_type_select" value="history"/>
439 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Merlin"/>
440 <param name="genome.ext" value="fasta"/>
441 </conditional>
442 <repeat name="track_groups">
443 <param name="category" value="Assembly properties"/>
444 <repeat name="data_tracks">
445 <conditional name="data_format">
446 <param name="data_format_select" value="gff"/>
447 <conditional name="useuri">
448 <param name="insource" value="history"/>
449 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.gff3"/>
450 </conditional>
451 </conditional>
452 </repeat>
453 <repeat name="data_tracks">
454 <conditional name="data_format">
455 <param name="data_format_select" value="bigwig"/>
456 <conditional name="useuri">
457 <param name="insource" value="history"/>
458 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.bw"/>
459 </conditional>
460 </conditional>
461 </repeat>
462 <repeat name="data_tracks">
463 <conditional name="data_format">
464 <param name="data_format_select" value="bed"/>
465 <conditional name="useuri">
466 <param name="insource" value="history"/>
467 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/test-6.bed"/>
468 </conditional>
469 </conditional>
470 </repeat>
471 <repeat name="data_tracks">
472 <conditional name="data_format">
473 <param name="data_format_select" value="vcf"/>
474 <conditional name="useuri">
475 <param name="insource" value="history"/>
476 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.vcf"/>
477 </conditional>
478 </conditional>
479 </repeat>
480 <repeat name="data_tracks">
481 <conditional name="data_format">
482 <param name="data_format_select" value="cram"/>
483 <conditional name="useuri">
484 <param name="insource" value="history"/>
485 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.cram"/>
486 </conditional>
487 </conditional>
488 </repeat>
489 <repeat name="data_tracks">
490 <conditional name="data_format">
491 <param name="data_format_select" value="bam"/>
492 <conditional name="useuri">
493 <param name="insource" value="history"/>
494 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin-sample.bam"/>
495 </conditional>
496 </conditional>
497 </repeat>
498 <repeat name="data_tracks">
499 <conditional name="data_format">
500 <param name="data_format_select" value="maf"/>
501 <conditional name="useuri">
502 <param name="insource" value="history"/>
503 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlinlastz.maf"/>
504 </conditional>
505 </conditional>
506 </repeat>
507 <repeat name="data_tracks">
508 <conditional name="data_format">
509 <param name="data_format_select" value="blastxml"/>
510 <conditional name="useuri">
511 <param name="insource" value="history"/>
512 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.blastxml"/>
513 </conditional>
514 </conditional>
515 </repeat>
516 <repeat name="data_tracks">
517 <conditional name="data_format">
518 <param name="data_format_select" value="bam"/>
519 <conditional name="useuri">
520 <param name="insource" value="history"/>
521 <param name="annotation" value=""/>
522 </conditional>
523 </conditional>
524 </repeat>
525 </repeat>
526 </repeat>
527 <repeat name="assemblies">
528 <conditional name="reference_genome">
529 <param name="genome_type_select" value="history"/>
530 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/dm3.fa"/>
531 <param name="genome.ext" value="fasta"/>
532 </conditional>
533 <repeat name="track_groups">
534 <param name="category" value="Assembly properties"/>
535 <repeat name="data_tracks">
536 <conditional name="data_format">
537 <param name="data_format_select" value="cool"/>
538 <conditional name="useuri">
539 <param name="insource" value="history"/>
540 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/dm3test.cool"/>
541 </conditional>
542 </conditional>
543 </repeat>
544 </repeat>
545 </repeat>
546 <repeat name="assemblies">
547 <conditional name="reference_genome">
548 <param name="genome_type_select" value="history"/>
549 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Ppersica1.fa"/>
550 <param name="genome.ext" value="fasta"/>
551 </conditional>
552 <repeat name="track_groups">
553 <param name="category" value="Assembly properties"/>
554 <repeat name="data_tracks">
555 <conditional name="data_format">
556 <param name="data_format_select" value="paf"/>
557 <conditional name="useuri">
558 <param name="insource" value="history"/>
559 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/peach-grape-map.paf"/>
560 </conditional>
561 <conditional name="pafuseuri">
562 <param name="insource" value="history"/>
563 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa"/>
564 </conditional>
565 </conditional>
566 </repeat>
567 <repeat name="data_tracks">
568 <conditional name="data_format">
569 <param name="data_format_select" value="paf"/>
570 <conditional name="useuri">
571 <param name="insource" value="history"/>
572 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabgrapepeach.paf"/>
573 </conditional>
574 <conditional name="pafuseuri">
575 <param name="insource" value="uri"/>
576 <repeat name="refuri">
577 <param name="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz"/>
578 <param name="annoname" value="arabidopsis.URI"/>
579 </repeat>
580 <repeat name="refuri">
581 <param name="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz"/>
582 <param name="annoname" value="Vvinifera1.URI"/>
583 </repeat>
584 </conditional>
585 </conditional>
586 </repeat>
587 <repeat name="data_tracks">
588 <conditional name="data_format">
589 <param name="data_format_select" value="paf"/>
590 <conditional name="useuri">
591 <param name="insource" value="history"/>
592 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabgrapepeach.paf"/>
593 </conditional>
594 <conditional name="pafuseuri">
595 <param name="insource" value="history"/>
596 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa"/>
597 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa"/>
598 </conditional>
599 </conditional>
600 </repeat>
601 </repeat>
602 </repeat>
603 <repeat name="assemblies">
604 <conditional name="reference_genome">
605 <param name="genome_type_select" value="uri"/>
606 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz"/>
607 <param name="refname" value="hg38"/>
608 </conditional>
609 <repeat name="track_groups">
610 <param name="category" value="Assembly properties"/>
611 <repeat name="data_tracks">
612 <conditional name="data_format">
613 <param name="data_format_select" value="hic"/>
614 <conditional name="useuri">
615 <param name="insource" value="uri"/>
616 <param name="annouri" value="https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic"/>
617 <param name="annoname" value="humanhic"/>
618 </conditional>
619 </conditional>
620 </repeat>
621 </repeat>
622 </repeat>
623 <section name="jbgen">
624 <param name="zipOut" value="true"/>
625 <param name="session_name" value="New test session"/>
626 </section>
627 <!-- use the following line to generate a ZIP file to inspect it -->
628 <!--output name="output" file="jbrowse2_result02.zip" ftype="zip" compare="sim_size"-->
629 <output name="output" ftype="zip">
630 <assert_contents>
631 <has_archive_member path=".*" n="637" delta="10"/>
632 <has_archive_member path="index.html"/>
633 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
634 <has_archive_member path="manifest.json">
635 <has_text text="favicon.ico"/>
636 <has_text text="background_color"/>
637 </has_archive_member>
638 <has_archive_member path="galaxy.xml">
639 <is_valid_xml/>
640 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/>
641 <element_text_is path="./metadata/general/session_name" text="New test session"/>
642 </has_archive_member>
643 <has_archive_member path="merlin.gff3_0.gz"/>
644 <has_archive_member path="merlin.gff3_0.gz.tbi"/>
645 <has_archive_member path="merlin.bw_1"/>
646 <has_archive_member path="test-6.bed_2.gz"/>
647 <has_archive_member path="merlin.vcf_3"/>
648 <has_archive_member path="merlin.vcf_3.tbi"/>
649 <has_archive_member path="merlin.cram_4"/>
650 <has_archive_member path="merlin.cram_4.crai"/>
651 <has_archive_member path="merlin-sample.bam_5"/>
652 <has_archive_member path="merlin-sample.bam_5.bai"/>
653 <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi"/>
654 <has_archive_member path="merlin.blastxml_7.gz"/>
655 <has_archive_member path="dm3test.cool_9.hic"/>
656 <has_archive_member path="peach-grape-map.paf_10"/>
657 <has_archive_member path="arabgrapepeach.paf_11"/>
658 <has_archive_member path="Merlin.fa.gz.fai"/>
659 <has_archive_member path="dm3.fa.fa.gz.fai"/>
660 <has_archive_member path="Ppersica1.fa.fa.gz"/>
661 <has_archive_member path="Ppersica1.fa.fa.gz.fai"/>
662 <has_archive_member path="Ppersica1.fa.fa.gz.gzi"/>
663 <has_archive_member path="Vvinifera1.fa.fa.gz.fai"/>
664 <has_archive_member path="Vvinifera1.fa.fa.gz"/>
665 <has_archive_member path="Vvinifera1.fa.fa.gz.gzi"/>
666 <has_archive_member path="config.json">
667 <has_json_property_with_text property="name" text="Merlin"/>
668 </has_archive_member>
669 </assert_contents>
670 </output>
671 </test>
672 <test>
673 <param name="autoCollection">
674 <collection type="list" name="merlintest">
675 <element name="merlin.fa" value="merlin.fa"/>
676 <element name="merlin.bw" value="bw/merlin.bw"/>
677 <element name="test-6.bed" value="bed/test-6.bed"/>
678 </collection>
679 </param>
680 <section name="jbgen">
681 <param name="zipOut" value="true"/>
682 <param name="session_name" value="Collection test"/>
683 <param name="ucol|formcoll" value="collect"/>
684 </section>
685 <!-- use the following line to generate a ZIP file to inspect it -->
686 <!--output name="output" file="jbrowse2_result01.zip" ftype="zip" compare="sim_size"-->
687 <output name="output" ftype="zip">
688 <assert_contents>
689 <has_archive_member path=".*" n="611" delta="10"/>
690 <has_archive_member path="index.html"/>
691 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
692 <has_archive_member path="manifest.json">
693 <has_text text="favicon.ico"/>
694 <has_text text="background_color"/>
695 </has_archive_member>
696 <has_archive_member path="galaxy.xml">
697 <is_valid_xml/>
698 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/>
699 <element_text_is path="./metadata/general/session_name" text="Collection test"/>
700 </has_archive_member>
701 <has_archive_member path="jb2_webserver.py"/>
702 <has_archive_member path="merlin.fa.fa.gz.gzi"/>
703 <has_archive_member path="merlin.fa.fa.gz"/>
704 <has_archive_member path="merlin.fa.fa.gz.fai"/>
705 <has_archive_member path="merlin.bw"/>
706 <has_archive_member path="index.html"/>
707 <has_archive_member path="test-6.bed.gz"/>
708 <has_archive_member path="test-6.bed.gz.tbi"/>
709 </assert_contents>
710 </output>
711 </test>
712 <test>
713 <repeat name="assemblies">
714 <conditional name="reference_genome">
715 <param name="genome_type_select" value="history"/>
716 <param name="genome" value="merlin.fa"/>
717 <param name="genome.ext" value="fasta"/>
718 <param name="genome.name" value="Merlin"/>
719 </conditional>
720 <repeat name="track_groups">
721 <param name="category" value="Default"/>
722 <repeat name="data_tracks">
723 <conditional name="data_format">
724 <param name="data_format_select" value="bigwig"/>
725 <conditional name="useuri">
726 <param name="annotation" value="bw/merlin.bw"/>
727 <param name="insource" value="history"/>
728 </conditional>
729 </conditional>
730 </repeat>
731 </repeat>
732 </repeat>
733 <section name="jbgen">
734 <param name="zipOut" value="true"/>
735 </section>
736 <output name="output">
737 <assert_contents>
738 <has_archive_member path="galaxy.xml">
739 <has_text text="genome path="/>
740 <has_text text="label="/>
741 <has_text text="format="/>
742 <has_text text="metadata"/>
743 <has_text text="useuri="/>
744 <has_text text="trackFile path="/>
745 <has_text text="ext=&quot;bigwig&quot;"/>
746 <has_text text="format=&quot;bigwig&quot;"/>
747 </has_archive_member>
748 </assert_contents>
749 </output>
750 </test>
751 <test>
752 <repeat name="assemblies">
753 <conditional name="reference_genome">
754 <param name="genome_type_select" value="history"/>
755 <param name="genome" value="merlin.fa"/>
756 <param name="genome.ext" value="fasta"/>
757 <param name="genome.name" value="Merlin"/>
758 </conditional>
759 <repeat name="track_groups">
760 <param name="category" value="Default"/>
761 <repeat name="data_tracks">
762 <conditional name="data_format">
763 <param name="data_format_select" value="vcf"/>
764 <conditional name="useuri">
765 <param name="insource" value="history"/>
766 <param name="annotation" value="vcf/merlin.vcf"/>
767 </conditional>
768 </conditional>
769 </repeat>
770 </repeat>
771 </repeat>
772 <section name="jbgen">
773 <param name="zipOut" value="true"/>
774 </section>
775 <output name="output">
776 <assert_contents>
777 <has_archive_member path="galaxy.xml">
778 <has_text text="genome path="/>
779 <has_text text="label="/>
780 <has_text text="format="/>
781 <has_text text="metadata"/>
782 <has_text text="useuri="/>
783 <has_text text="trackFile path="/>
784 <has_text text="ext=&quot;vcf&quot; label=&quot;merlin.vcf&quot;"/>
785 </has_archive_member>
786 </assert_contents>
787 </output>
788 </test>
789 <test>
790 <repeat name="assemblies">
791 <conditional name="reference_genome">
792 <param name="genome_type_select" value="history"/>
793 <param name="genome" value="merlin.fa"/>
794 <param name="genome.ext" value="fasta"/>
795 <param name="genome.name" value="Merlin"/>
796 </conditional>
797 </repeat>
798 <section name="jbgen">
799 <param name="zipOut" value="true"/>
800 </section>
801 <output name="output">
802 <assert_contents>
803 <has_archive_member path="galaxy.xml">
804 <has_text text="genome path="/>
805 <has_text text="label="/>
806 <has_text text="useuri="/>
807 <has_text text="metadata"/>
808 </has_archive_member>
809 </assert_contents>
810 </output>
811 </test>
812 <test>
813 <repeat name="assemblies">
814 <conditional name="reference_genome">
815 <param name="genome_type_select" value="history"/>
816 <param name="genome" value="merlin.fa"/>
817 <param name="genome.ext" value="fasta"/>
818 <param name="genome.name" value="Merlin"/>
819 </conditional>
820 <repeat name="track_groups">
821 <param name="category" value="Default"/>
822 <repeat name="data_tracks">
823 <conditional name="data_format">
824 <param name="data_format_select" value="vcf"/>
825 <conditional name="useuri">
826 <param name="insource" value="history"/>
827 <param name="annotation" value="vcf/merlin.vcf"/>
828 </conditional>
829 </conditional>
830 </repeat>
831 </repeat>
832 </repeat>
833 <section name="jbgen">
834 <param name="zipOut" value="true"/>
835 </section>
836 <output name="output">
837 <assert_contents>
838 <has_archive_member path="galaxy.xml">
839 <has_text text="genome path="/>
840 <has_text text="label="/>
841 <has_text text="format="/>
842 <has_text text="metadata"/>
843 <has_text text="useuri="/>
844 <has_text text="trackFile path="/>
845 <has_text text="ext=&quot;vcf&quot; label=&quot;merlin.vcf&quot;"/>
846 </has_archive_member>
847 </assert_contents>
848 </output>
849 </test>
850 <test>
851 <repeat name="assemblies">
852 <conditional name="reference_genome">
853 <param name="genome_type_select" value="history"/>
854 <param name="genome" value="merlin.fa"/>
855 <param name="genome.ext" value="fasta"/>
856 <param name="genome.name" value="Merlin"/>
857 </conditional>
858 <repeat name="track_groups">
859 <param name="category" value="Default"/>
860 <repeat name="data_tracks">
861 <conditional name="data_format">
862 <param name="data_format_select" value="gff"/>
863 <conditional name="useuri">
864 <param name="insource" value="history"/>
865 <param name="annotation" value="gff3/A.gff"/>
866 </conditional>
867 </conditional>
868 <conditional name="match_part">
869 <param name="match_part_select" value="false"/>
870 </conditional>
871 <section name="jbcolor_scale">
872 <conditional name="color_score">
873 <param name="color_score_select" value="none"/>
874 </conditional>
875 <conditional name="color">
876 <param name="color_select" value="automatic"/>
877 </conditional>
878 </section>
879 </repeat>
880 </repeat>
881 <repeat name="track_groups">
882 <param name="category" value="Ignore Scale"/>
883 <repeat name="data_tracks">
884 <conditional name="data_format">
885 <param name="data_format_select" value="gff"/>
886 <conditional name="useuri">
887 <param name="insource" value="history"/>
888 <param name="annotation" value="gff3/1.gff"/>
889 </conditional>
890 <conditional name="match_part">
891 <param name="match_part_select" value="false"/>
892 </conditional>
893 <section name="jbcolor_scale">
894 <conditional name="color_score">
895 <param name="color_score_select" value="none"/>
896 <conditional name="color">
897 <param name="color_select" value="manual"/>
898 <param name="style_color" value="#ff00ff"/>
899 </conditional>
900 </conditional>
901 </section>
902 </conditional>
903 </repeat>
904 </repeat>
905 <repeat name="track_groups">
906 <param name="category" value="Scaled Colour"/>
907 <repeat name="data_tracks">
908 <conditional name="data_format">
909 <param name="data_format_select" value="gff"/>
910 <conditional name="useuri">
911 <param name="insource" value="history"/>
912 <param name="annotation" value="gff3/C.gff"/>
913 </conditional>
914 <conditional name="match_part">
915 <param name="match_part_select" value="false"/>
916 </conditional>
917 <section name="jbcolor_scale">
918 <conditional name="color_score">
919 <param name="color_score_select" value="score"/>
920 <param name="score_scaling" value="linear"/>
921 <conditional name="score_scales">
922 <param name="scale_select" value="automatic"/>
923 </conditional>
924 <conditional name="color_scheme">
925 <param name="score_scheme" value="opacity"/>
926 <conditional name="color">
927 <param name="color_select" value="automatic"/>
928 </conditional>
929 </conditional>
930 </conditional>
931 </section>
932 </conditional>
933 </repeat>
934 <repeat name="data_tracks">
935 <conditional name="data_format">
936 <param name="data_format_select" value="gff"/>
937 <conditional name="useuri">
938 <param name="annotation" value="gff3/B.gff"/>
939 <param name="insource" value="history"/>
940 </conditional>
941 <conditional name="match_part">
942 <param name="match_part_select" value="false"/>
943 </conditional>
944 <section name="jbcolor_scale">
945 <conditional name="color_score">
946 <param name="color_score_select" value="score"/>
947 <param name="score_scaling" value="linear"/>
948 <conditional name="score_scales">
949 <param name="scale_select" value="automatic"/>
950 </conditional>
951 <conditional name="color_scheme">
952 <param name="score_scheme" value="opacity"/>
953 <conditional name="color">
954 <param name="color_select" value="manual"/>
955 <param name="style_color" value="#0000ff"/>
956 </conditional>
957 </conditional>
958 </conditional>
959 </section>
960 </conditional>
961 </repeat>
962 <repeat name="data_tracks">
963 <conditional name="data_format">
964 <param name="data_format_select" value="gff"/>
965 <conditional name="useuri">
966 <param name="annotation" value="gff3/A.gff"/>
967 <param name="insource" value="history"/>
968 </conditional>
969 <conditional name="match_part">
970 <param name="match_part_select" value="false"/>
971 </conditional>
972 <section name="jbcolor_scale">
973 <conditional name="color_score">
974 <param name="color_score_select" value="score"/>
975 <param name="score_scaling" value="linear"/>
976 <conditional name="score_scales">
977 <param name="scale_select" value="manual"/>
978 <param name="minimum" value="0"/>
979 <param name="maximum" value="1000"/>
980 </conditional>
981 <conditional name="color_scheme">
982 <param name="score_scheme" value="opacity"/>
983 <conditional name="color">
984 <param name="color_select" value="automatic"/>
985 </conditional>
986 </conditional>
987 </conditional>
988 </section>
989 </conditional>
990 </repeat>
991 <repeat name="data_tracks">
992 <conditional name="data_format">
993 <param name="data_format_select" value="gff"/>
994 <conditional name="useuri">
995 <param name="annotation" value="gff3/1.gff"/>
996 <param name="insource" value="history"/>
997 </conditional>
998 <conditional name="match_part">
999 <param name="match_part_select" value="false"/>
1000 </conditional>
1001 <section name="jbcolor_scale">
1002 <conditional name="color_score">
1003 <param name="color_score_select" value="score"/>
1004 <param name="score_scaling" value="linear"/>
1005 <conditional name="score_scales">
1006 <param name="scale_select" value="manual"/>
1007 <param name="minimum" value="0"/>
1008 <param name="maximum" value="1000"/>
1009 </conditional>
1010 <conditional name="color_scheme">
1011 <param name="score_scheme" value="opacity"/>
1012 <conditional name="color">
1013 <param name="color_select" value="manual"/>
1014 <param name="style_color" value="#ff0000"/>
1015 </conditional>
1016 </conditional>
1017 </conditional>
1018 </section>
1019 </conditional>
1020 </repeat>
1021 </repeat>
1022 <repeat name="track_groups">
1023 <param name="category" value="Realistic"/>
1024 <repeat name="data_tracks">
1025 <conditional name="data_format">
1026 <param name="data_format_select" value="gff"/>
1027 <conditional name="useuri">
1028 <param name="annotation" value="gff3/interpro.gff"/>
1029 <param name="insource" value="history"/>
1030 </conditional>
1031 <conditional name="match_part">
1032 <param name="match_part_select" value="false"/>
1033 </conditional>
1034 <section name="jbcolor_scale">
1035 <conditional name="color_score">
1036 <param name="color_score_select" value="none"/>
1037 </conditional>
1038 <conditional name="color">
1039 <param name="color_select" value="automatic"/>
1040 </conditional>
1041 </section>
1042 </conditional>
1043 </repeat>
1044 <repeat name="data_tracks">
1045 <conditional name="data_format">
1046 <param name="data_format_select" value="gff"/>
1047 <conditional name="useuri">
1048 <param name="annotation" value="gff3/2.gff"/>
1049 <param name="insource" value="history"/>
1050 </conditional>
1051 <conditional name="match_part">
1052 <param name="match_part_select" value="true"/>
1053 <param name="name" value="cDNA_match"/>
1054 </conditional>
1055 <section name="jbcolor_scale">
1056 <conditional name="color_score">
1057 <param name="color_score_select" value="none"/>
1058 </conditional>
1059 <conditional name="color">
1060 <param name="color_select" value="automatic"/>
1061 </conditional>
1062 </section>
1063 </conditional>
1064 </repeat>
1065 </repeat>
1066 </repeat>
1067 <section name="jbgen">
1068 <param name="zipOut" value="true"/>
1069 </section>
1070 <output name="output">
1071 <assert_contents>
1072 <has_archive_member path="A.gff"/>
1073 <has_archive_member path="B.gff"/>
1074 <has_archive_member path="C.gff"/>
1075 <has_archive_member path="interpro.gff"/>
1076 <has_archive_member path="1.gff"/>
1077 <has_archive_member path="2.gff"/>
1078 <has_archive_member path="galaxy.xml">
1079 <is_valid_xml/>
1080 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/>
1081 <element_text_is path="./metadata/general/session_name" text="New JBrowse2 session"/>
1082 </has_archive_member>
1083 </assert_contents>
1084 </output>
1085 </test>
1086 <test>
1087 <repeat name="assemblies">
1088 <conditional name="reference_genome">
1089 <param name="genome_type_select" value="history"/>
1090 <param name="genome" value="merlin.fa"/>
1091 </conditional>
1092 <repeat name="track_groups">
1093 <param name="category" value="Auto Coloured"/>
1094 <repeat name="data_tracks">
1095 <conditional name="data_format">
1096 <param name="data_format_select" value="cram"/>
1097 <param name="annotation" value="cram/merlin-sample.cram"/>
1098 </conditional>
1099 </repeat>
1100 </repeat>
1101 </repeat>
1102 <section name="jbgen">
1103 <param name="zipOut" value="true"/>
1104 </section>
1105 <output name="output" ftype="zip">
1106 <assert_contents>
1107 <!-- roughly 590 files in an archive -->
1108 <has_archive_member path=".*" n="608" delta="30"/>
1109 <has_archive_member path="index.html"/>
1110 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
1111 <has_archive_member path="manifest.json">
1112 <has_text text="favicon.ico"/>
1113 <has_text text="background_color"/>
1114 </has_archive_member>
1115 <has_archive_member path="merlin.fa.fa.gz.fai"/>
1116 <has_archive_member path="galaxy.xml">
1117 <is_valid_xml/>
1118 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/>
1119 <element_text_is path="./metadata/general/session_name" text="New JBrowse2 session"/>
1120 </has_archive_member>
1121 </assert_contents>
1122 </output>
1123 </test>
1124 </tests>
1125 <help><![CDATA[
1126
1127 JBrowse2-in-Galaxy
1128 ==================
1129
1130 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible Genome viewer.
1131
1132 Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes,
1133 and detailed track styling is not yet implemented. Please contact us if you are missing features.
1134
1135 Use and local viewing
1136 =====================
1137
1138
1139 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
1140
1141 The same browser data and setup can also be downloaded as a compressed zip archive by clicking the download ("floppy disk") icon in the history.
1142 This can be shared and viewed without Galaxy.
1143
1144 A replacement application to serve the browser is required without Galaxy. A local python web server can be started using a script included in each archive,
1145 assuming that Python3 is already working on your desktop - if not you will have to install it first. Unzip the archive (*unzip [filename].zip*) and change
1146 directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*
1147
1148 With python3 installed,
1149
1150 *python3 jb2_webserver.py*
1151
1152 will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open,
1153 but the script appears to be running, try pointing your web browser to the default of *localhost:8080*
1154
1155 Overview
1156 --------
1157
1158 JBrowse is a fast, embeddable genome browser built completely with
1159 JavaScript and HTML5.
1160
1161 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
1162 JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying
1163 about how to run the command line tools to format your data, and which
1164 options need to be supplied and where.
1165
1166 Options
1167 -------
1168
1169 **Reference or Assembly**
1170
1171 Choose either a built-in or select one from your history.
1172
1173 Track coordinates and contig names *must* match this reference precisely
1174 or they will not display.
1175
1176 **Track Groups** represent a set of tracks in a single category.
1177
1178 Annotation Tracks
1179 -----------------
1180
1181 MAF
1182 ~~~
1183
1184 For history references, the name of the reference genome dataset in your history is very important for MAF tracks,
1185 because it becomes the "dbkey" for that reference. So, it must be exactly the same as the genome name (dbkey) used
1186 when making the MAF, typically in the Lastz tool.
1187
1188 If you used "hg38" as the reference in Lastz, that is exactly what the reference fasta should be named for any MAF track.
1189 Change it using the "pencil" icon on the reference data in your history. Any other name, such as "hg38.fasta"
1190 will cause the MAF track to show no data since there are no matches with that reference dbkey.
1191
1192
1193 GFF3/BED
1194 ~~~~~~~~
1195
1196 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region.
1197
1198 When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads
1199 to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is
1200 selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works
1201 well for relatively sparse bed files. A better option is to make a bigwig track using a set of windows based on the
1202 lengths of each assembly or reference contig.
1203
1204 BAM Pileups
1205 ~~~~~~~~~~~
1206
1207 We support BAM files and can automatically generate SNP tracks based on
1208 that bam data.
1209
1210
1211 BlastXML
1212 ~~~~~~~~
1213
1214 JiG now supports both blastn and blastp datasets. JiG internally uses a
1215 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
1216 format amenable to visualization in JBrowse. This tool is also
1217 available separately from the IUC on the toolshed.
1218
1219 **Minimum Gap Size** reflects how long a gap must be before it becomes a
1220 real gap in the processed gff3 file. In the picture above, various sizes
1221 of gaps can be seen. If the minimum gap size was set much higher, say
1222 100nt, many of the smaller gaps would disappear, and the features on
1223 both sides would be merged into one, longer feature. This setting is
1224 inversely proportional to runtime and output file size. *Do not set this
1225 to a low value for large datasets*. By setting this number lower, you
1226 will have extremely large outputs and extremely long runtimes. The
1227 default was configured based off of the author's experience, but the
1228 author only works on small viruses. It is *strongly* recommended that
1229 you filter your blast results before display, e.g. picking out the top
1230 10 hits or so.
1231
1232 **Protein blast search** option merely informs underlying tools that
1233 they should adjust feature locations by 3x.
1234
1235
1236 ]]></help>
1237 <expand macro="citations"/>
1238 <expand macro="creators"/>
1239 </tool>