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comparison jbrowse2.xml @ 134:ed3a21033188 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bb6736899ac3029f73455637a04a006fcd857fc2
author bgruening
date Sun, 20 Oct 2024 07:11:16 +0000
parents cec274db51c0
children
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133:cec274db51c0 134:ed3a21033188
8 <xref type="bio.tools">jbrowse_2</xref> 8 <xref type="bio.tools">jbrowse_2</xref>
9 </xrefs> 9 </xrefs>
10 <expand macro="requirements"/> 10 <expand macro="requirements"/>
11 <required_files> 11 <required_files>
12 <include path="autogenJB2.py"/> 12 <include path="autogenJB2.py"/>
13 <include path="blastxml_to_gapped_gff3.py"/>
14 <include path="convertMAF.sh"/> 13 <include path="convertMAF.sh"/>
15 <include path="gff3_rebase.py"/>
16 <include path="jb2_webserver.py"/> 14 <include path="jb2_webserver.py"/>
17 <include path="jbrowse2.py"/> 15 <include path="jbrowse2.py"/>
18 <include path="maf2bed.py"/> 16 <include path="maf2bed.py"/>
19 <include path="bedscoreplugin.js"/> 17 <include path="bedscoreplugin.js"/>
20 </required_files> 18 </required_files>
98 <dataset 96 <dataset
99 dname = "${assembly.reference_genome.refname}" /> 97 dname = "${assembly.reference_genome.refname}" />
100 </metadata> 98 </metadata>
101 </genome> 99 </genome>
102 #else if str($assembly.reference_genome.genome_type_select) == "indexed": 100 #else if str($assembly.reference_genome.genome_type_select) == "indexed":
103 <genome path="${assembly.reference_genome.genome.fields.path}" label="${assembly.reference_genome.genome.fields.dbkey}" useuri="no"> 101 <genome path="${assembly.reference_genome.indexed.fields.path}" label="${assembly.reference_genome.indexed.fields.dbkey}" useuri="no">
104 <metadata> 102 <metadata>
105 <dataset 103 <dataset
106 dname = "${assembly.reference_genome.genome.fields.name}" /> 104 dname = "${assembly.reference_genome.indexed.fields.name}" />
107 </metadata> 105 </metadata>
108 </genome> 106 </genome>
109 #else 107 #else
110 <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.element_identifier}" useuri="no"> 108 <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.element_identifier}" useuri="no">
111 <metadata> 109 <metadata>
212 #end if 210 #end if
213 #end if 211 #end if
214 #if $input_exists == "True": 212 #if $input_exists == "True":
215 <options> 213 <options>
216 <style> 214 <style>
217 #if str($track.data_format.data_format_select) in ["gff", "bed", "maf", "blastxml"]: 215 #if str($track.data_format.data_format_select) in ["gff", "bed", "maf"]:
218 <type>${track.data_format.jbstyle.display}</type> 216 <type>${track.data_format.jbstyle.display}</type>
219 #if str($track.data_format.jbstyle.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]: 217 #if str($track.data_format.jbstyle.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
220 <trackShowLabels>${track.data_format.jbstyle.show_labels}</trackShowLabels> 218 <trackShowLabels>${track.data_format.jbstyle.show_labels}</trackShowLabels>
221 <trackShowDescriptions>${track.data_format.jbstyle.show_descriptions}</trackShowDescriptions> 219 <trackShowDescriptions>${track.data_format.jbstyle.show_descriptions}</trackShowDescriptions>
222 #end if 220 #end if
244 #if str($track.data_format.data_format_select) in ["hic", "cool", "mcool", "scool"]: 242 #if str($track.data_format.data_format_select) in ["hic", "cool", "mcool", "scool"]:
245 <type>LinearHicDisplay</type> 243 <type>LinearHicDisplay</type>
246 #end if 244 #end if
247 </style> 245 </style>
248 #if str($track.data_format.data_format_select) == "bam": 246 #if str($track.data_format.data_format_select) == "bam":
249 <bam> 247 #if str($track.data_format.useuri.insource) == "history":
250 <bam_index> 248 <bam>
251 #for $dataset in $track.data_format.useuri.annotation: 249 <bam_index>
252 ${dataset} ~ ${dataset.metadata.bam_index}, 250 #for $dataset in $track.data_format.useuri.annotation:
253 #end for 251 ${dataset}~~~${dataset.metadata.bam_index},
254 </bam_index> 252 #end for
255 </bam> 253 </bam_index>
254 </bam>
255 #end if
256 #else if str($track.data_format.data_format_select) == "cram": 256 #else if str($track.data_format.data_format_select) == "cram":
257 <cram> 257 #if str($track.data_format.useuri.insource) == "history":
258 <cram_index> 258 <cram>
259 #for $dataset in $track.data_format.useuri.annotation: 259 <cram_index>
260 ${dataset} ~ ${dataset.metadata.cram_index}, 260 #for $dataset in $track.data_format.useuri.annotation:
261 #end for 261 ${dataset}~~~${dataset.metadata.cram_index},
262 </cram_index> 262 #end for
263 </cram> 263 </cram_index>
264 #else if str($track.data_format.data_format_select) == "blastxml": 264 </cram>
265 <blast> 265 #end if
266 #if str($track.data_format.blast_parent) != "":
267 <parent>${track.data_format.blast_parent}</parent>
268 #end if
269 <protein>${track.data_format.is_protein}</protein>
270 <min_gap>${track.data_format.min_gap}</min_gap>
271 </blast>
272 #else if str($track.data_format.data_format_select) == "gff": 266 #else if str($track.data_format.data_format_select) == "gff":
273 <gff> 267 <gff>
274 #if $track.data_format.match_part.match_part_select == "true": 268 #if $track.data_format.match_part.match_part_select == "true":
275 <match>${track.data_format.match_part.name}</match> 269 <match>${track.data_format.match_part.name}</match>
276 #end if 270 #end if
278 #else if str($track.data_format.data_format_select) == "paf": 272 #else if str($track.data_format.data_format_select) == "paf":
279 <paf> 273 <paf>
280 #if str($track.data_format.pafuseuri.insource) == "history": 274 #if str($track.data_format.pafuseuri.insource) == "history":
281 <genome> 275 <genome>
282 #for $anno in $track.data_format.pafuseuri.annotation: 276 #for $anno in $track.data_format.pafuseuri.annotation:
283 ${anno} ~ ${anno.name}, 277 #set nospaces = $anno.element_identifier.replace(' ','')
278 ${anno}~~~${nospaces},
284 #end for 279 #end for
285 </genome> 280 </genome>
286 <useuri> 281 <useuri>
287 false 282 false
288 </useuri> 283 </useuri>
289 #else: 284 #else:
290 <genome> 285 <genome>
291 #for $refgenome in $track.data_format.pafuseuri.refuri: 286 #for $refgenome in $track.data_format.pafuseuri.refuri:
292 ${refgenome.annotation} ~ ${refgenome.annoname}, 287 #set nospaces = $refgenome.refname.replace(' ','')
288 ${refgenome.uri}~~~${nospaces},
293 #end for 289 #end for
294 </genome> 290 </genome>
295 <useuri> 291 <useuri>
296 true 292 true
297 </useuri> 293 </useuri>
335 <option value="history">Use a genome fasta file from the current history</option> 331 <option value="history">Use a genome fasta file from the current history</option>
336 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as 332 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as
337 tabix bgzip with predictable index file URI</option> 333 tabix bgzip with predictable index file URI</option>
338 </param> 334 </param>
339 <when value="indexed"> 335 <when value="indexed">
340 <param name="genome" type="select" optional="false" 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"> 336 <param name="indexed" type="select" optional="false" label="Select a built in reference genome or custom genome"
337 help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome">
341 <options from_data_table="all_fasta"> 338 <options from_data_table="all_fasta">
342 <filter column="2" type="sort_by"/> 339 <filter column="2" type="sort_by"/>
343 <validator message="No genomes are available for the selected input dataset" type="no_options"/> 340 <validator message="No genomes are available for the selected input dataset" type="no_options"/>
344 </options> 341 </options>
345 </param> 342 </param>
353 </param> 350 </param>
354 <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"/> 351 <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"/>
355 </when> 352 </when>
356 </conditional> 353 </conditional>
357 <repeat name="track_groups" title="Track Group"> 354 <repeat name="track_groups" title="Track Group">
358 <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."/> 355 <param name="category" type="text" value="Default" optional="False" label="Track Category"
356 help="Organise your tracks into Categories for a nicer end-user experience. #date# is replaced with current date"/>
359 <repeat name="data_tracks" title="Annotation Track"> 357 <repeat name="data_tracks" title="Annotation Track">
360 <conditional name="data_format" label="Track Data Selection Options"> 358 <conditional name="data_format" label="Track Data Selection Options">
361 <param name="data_format_select" type="select" label="Track Type"> 359 <param name="data_format_select" type="select" label="Track Type">
362 <option value="bam">BAM track. Recommend converting to BED/bigWig unless mapping annotation needed</option> 360 <option value="bam">BAM track. Recommend converting to BED/bigWig unless mapping annotation needed</option>
363 <option value="bed">BED track</option> 361 <option value="bed">BED track</option>
364 <option value="bigwig">BigWig track</option> 362 <option value="bigwig">BigWig track</option>
365 <option value="blastxml">Blast XML track (as GFF3)</option>
366 <option value="cram">CRAM track. Recommend converting to BED/bigWig unless mapping annotation needed</option> 363 <option value="cram">CRAM track. Recommend converting to BED/bigWig unless mapping annotation needed</option>
367 <option value="gff">GFF/GFF3 track</option> 364 <option value="gff">GFF/GFF3 track</option>
368 <option value="cool">HiC as cool/mcool/scool format files</option> 365 <option value="cool">HiC as cool/mcool/scool format files</option>
369 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> 366 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
370 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option> 367 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
371 <option value="paf">PAF - Pairwise approximate mapping positions between two set of sequences</option> 368 <option value="paf">PAF - Pairwise approximate mapping positions between two set of sequences</option>
372 <option value="vcf">VCF SNP track</option> 369 <option value="vcf">VCF SNP track</option>
373 </param> 370 </param>
374 <when value="blastxml">
375 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml"/>
376 <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."/>
377 <param name="min_gap" type="integer" min="2" value="10" label="Minimum Gap Size" help="before a new match_part feature is created"/>
378 <param name="is_protein" type="boolean" truevalue="true" falsevalue="false" label="Is this a protein blast search?"/>
379 <expand macro="track_styling_vgp"/>
380 <expand macro="track_visibility"/>
381 </when>
382 <when value="vcf"> 371 <when value="vcf">
383 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip"/> 372 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip"/>
384 <expand macro="track_styling_vcf"/> 373 <expand macro="track_styling_vcf"/>
385 <expand macro="track_visibility"/> 374 <expand macro="track_visibility"/>
386 </when> 375 </when>
519 <param name="insource" value="history"/> 508 <param name="insource" value="history"/>
520 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlinlastz.maf"/> 509 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlinlastz.maf"/>
521 </conditional> 510 </conditional>
522 </conditional> 511 </conditional>
523 </repeat> 512 </repeat>
524 <repeat name="data_tracks">
525 <conditional name="data_format">
526 <param name="data_format_select" value="blastxml"/>
527 <conditional name="useuri">
528 <param name="insource" value="history"/>
529 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.blastxml"/>
530 </conditional>
531 </conditional>
532 </repeat>
533 <repeat name="data_tracks">
534 <conditional name="data_format">
535 <param name="data_format_select" value="bam"/>
536 <conditional name="useuri">
537 <param name="insource" value="history"/>
538 <param name="annotation" value=""/>
539 </conditional>
540 </conditional>
541 </repeat>
542 </repeat> 513 </repeat>
543 </repeat> 514 </repeat>
544 <repeat name="assemblies"> 515 <repeat name="assemblies">
545 <conditional name="reference_genome"> 516 <conditional name="reference_genome">
546 <param name="genome_type_select" value="history"/> 517 <param name="genome_type_select" value="history"/>
589 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabgrapepeach.paf"/> 560 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabgrapepeach.paf"/>
590 </conditional> 561 </conditional>
591 <conditional name="pafuseuri"> 562 <conditional name="pafuseuri">
592 <param name="insource" value="uri"/> 563 <param name="insource" value="uri"/>
593 <repeat name="refuri"> 564 <repeat name="refuri">
594 <param name="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz"/> 565 <param name="uri" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz"/>
595 <param name="annoname" value="arabidopsis.URI"/> 566 <param name="refname" value="arabidopsis.URI"/>
596 </repeat> 567 </repeat>
597 <repeat name="refuri"> 568 <repeat name="refuri">
598 <param name="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz"/> 569 <param name="uri" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz"/>
599 <param name="annoname" value="Vvinifera1.URI"/> 570 <param name="refname" value="Vvinifera1.URI"/>
600 </repeat> 571 </repeat>
601 </conditional> 572 </conditional>
602 </conditional> 573 </conditional>
603 </repeat> 574 </repeat>
604 <repeat name="data_tracks"> 575 <repeat name="data_tracks">
641 <param name="zipOut" value="true"/> 612 <param name="zipOut" value="true"/>
642 <param name="session_name" value="New test session"/> 613 <param name="session_name" value="New test session"/>
643 </section> 614 </section>
644 <output name="output" ftype="zip"> 615 <output name="output" ftype="zip">
645 <assert_contents> 616 <assert_contents>
646 <has_archive_member path=".*" n="678" delta="10"/> 617 <has_archive_member path=".*" n="676" delta="10"/>
647 <has_archive_member path="index.html"/> 618 <has_archive_member path="index.html"/>
648 <has_archive_member path="manifest.json"> 619 <has_archive_member path="manifest.json">
649 <has_text text="favicon.ico"/> 620 <has_text text="favicon.ico"/>
650 <has_text text="background_color"/> 621 <has_text text="background_color"/>
651 </has_archive_member> 622 </has_archive_member>
663 <has_archive_member path="merlin.cram_4"/> 634 <has_archive_member path="merlin.cram_4"/>
664 <has_archive_member path="merlin.cram_4.crai"/> 635 <has_archive_member path="merlin.cram_4.crai"/>
665 <has_archive_member path="merlin-sample.bam_5"/> 636 <has_archive_member path="merlin-sample.bam_5"/>
666 <has_archive_member path="merlin-sample.bam_5.bai"/> 637 <has_archive_member path="merlin-sample.bam_5.bai"/>
667 <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi"/> 638 <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi"/>
668 <has_archive_member path="merlin.blastxml_7.gz"/> 639 <has_archive_member path="dm3test.cool_7.hic"/>
669 <has_archive_member path="dm3test.cool_9.hic"/> 640 <has_archive_member path="peach-grape-map.paf_8"/>
670 <has_archive_member path="peach-grape-map.paf_10"/> 641 <has_archive_member path="arabgrapepeach.paf_10"/>
671 <has_archive_member path="arabgrapepeach.paf_11"/>
672 <has_archive_member path="Merlin.fa.gz.fai"/> 642 <has_archive_member path="Merlin.fa.gz.fai"/>
673 <has_archive_member path="dm3.fa.fa.gz.fai"/> 643 <has_archive_member path="dm3.fa.fa.gz.fai"/>
674 <has_archive_member path="Ppersica1.fa.fa.gz"/> 644 <has_archive_member path="Ppersica1.fa.fa.gz"/>
675 <has_archive_member path="Ppersica1.fa.fa.gz.fai"/> 645 <has_archive_member path="Ppersica1.fa.fa.gz.fai"/>
676 <has_archive_member path="Ppersica1.fa.fa.gz.gzi"/> 646 <has_archive_member path="Ppersica1.fa.fa.gz.gzi"/>
1197 :: 1167 ::
1198 1168
1199 bam 1169 bam
1200 bed 1170 bed
1201 bigwig 1171 bigwig
1202 blastxml
1203 cram 1172 cram
1204 gff3 1173 gff3
1205 hic 1174 hic
1206 maf 1175 maf
1207 paf 1176 paf
1208 vcf 1177 vcf
1209 1178
1179 Blastxml was deprecated in JBrowse 2.15.4 because the emitted GFF fails validation and will not display
1210 Note that cram and bam will be large, so very slow amd are only recommended if you need the cigar annotation. Otherwise conversion to bed is recommended to slim them down. 1180 Note that cram and bam will be large, so very slow amd are only recommended if you need the cigar annotation. Otherwise conversion to bed is recommended to slim them down.
1211 Unfortunately if you have millions of rows in a bed, it will also be very slow - in which case a bigwig is recommended. 1181 Unfortunately if you have millions of rows in a bed, it will also be very slow - in which case a bigwig is recommended.
1212 1182
1213 A JBrowse2 history item can be opened by viewing it (the "eye" icon). 1183 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
1214 1184
1281 1251
1282 1252
1283 BlastXML 1253 BlastXML
1284 ~~~~~~~~ 1254 ~~~~~~~~
1285 1255
1286 JiG now supports both blastn and blastp datasets. JiG internally uses a 1256 Deprecated in 2.15.4 because the new GFF parser rejects the output of the
1287 blastXML to gapped GFF3 tool to convert your blastxml datasets into a 1257 original JBrowse1 blastxml to gff converter.
1288 format amenable to visualization in JBrowse. This tool is also
1289 available separately from the IUC on the toolshed.
1290
1291 **Minimum Gap Size** reflects how long a gap must be before it becomes a
1292 real gap in the processed gff3 file. In the picture above, various sizes
1293 of gaps can be seen. If the minimum gap size was set much higher, say
1294 100nt, many of the smaller gaps would disappear, and the features on
1295 both sides would be merged into one, longer feature. This setting is
1296 inversely proportional to runtime and output file size. *Do not set this
1297 to a low value for large datasets*. By setting this number lower, you
1298 will have extremely large outputs and extremely long runtimes. The
1299 default was configured based off of the author's experience, but the
1300 author only works on small viruses. It is *strongly* recommended that
1301 you filter your blast results before display, e.g. picking out the top
1302 10 hits or so.
1303
1304 **Protein blast search** option merely informs underlying tools that
1305 they should adjust feature locations by 3x.
1306 1258
1307 Local viewing 1259 Local viewing
1308 ============= 1260 =============
1309 1261
1310 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. 1262 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.