Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.xml @ 48:460d5b6c5d98 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
author fubar
date Wed, 06 Mar 2024 10:37:49 +0000
parents 4181e97c70a7
children bdfa6a7c4543
comparison
equal deleted inserted replaced
47:3e53204c2419 48:460d5b6c5d98
136 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl> 136 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
137 </metadata> 137 </metadata>
138 <tracks> 138 <tracks>
139 #for $tg in $track_groups: 139 #for $tg in $track_groups:
140 #for $track in $tg.data_tracks: 140 #for $track in $tg.data_tracks:
141 #if $track.data_format.useuri.insource == "history": 141 #if $track.data_format.useuri.insource == "uri":
142 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
143 <files>
144 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" label="${track.data_format.useuri.annoname}" useuri="yes">
145 <metadata>
146 <dataset id = "${track.data_format.useuri.annouri}" />
147 </metadata>
148 </trackFile>
149 </files>
150 <options/>
151 </track>
152 #else if $track.data_format.useuri.insource == "history":
142 #if $track.data_format.useuri.annotation: 153 #if $track.data_format.useuri.annotation:
143 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> 154 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
144 <files> 155 <files>
145 #for $dataset in $track.data_format.useuri.annotation: 156 #for $dataset in $track.data_format.useuri.annotation:
146 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no"> 157 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no">
202 <parent>${track.data_format.blast_parent}</parent> 213 <parent>${track.data_format.blast_parent}</parent>
203 #end if 214 #end if
204 <protein>${track.data_format.is_protein}</protein> 215 <protein>${track.data_format.is_protein}</protein>
205 <min_gap>${track.data_format.min_gap}</min_gap> 216 <min_gap>${track.data_format.min_gap}</min_gap>
206 </blast> 217 </blast>
207 #else if str($track.data_format.data_format_select) == "gene_calls": 218 #else if str($track.data_format.data_format_select) == "gff":
208 <gff> 219 <gff>
209 #if $track.data_format.match_part.match_part_select == "true": 220 #if $track.data_format.match_part.match_part_select == "true":
210 <match>${track.data_format.match_part.name}</match> 221 <match>${track.data_format.match_part.name}</match>
211 #end if 222 #end if
212 </gff> 223 </gff>
227 <hic> 238 <hic>
228 </hic> 239 </hic>
229 #else if str($track.data_format.data_format_select) == "cool": 240 #else if str($track.data_format.data_format_select) == "cool":
230 <cool> 241 <cool>
231 </cool> 242 </cool>
243 #else if str($track.data_format.data_format_select) == "bed":
244 <bed>
245 </bed>
232 #else if str($track.data_format.data_format_select) == "sparql": 246 #else if str($track.data_format.data_format_select) == "sparql":
233 <label>${track.data_format.label}</label> 247 <label>${track.data_format.label}</label>
234 <sparql> 248 <sparql>
235 <url>${track.data_format.url}</url> 249 <url>${track.data_format.url}</url>
236 <query>${track.data_format.query}</query> 250 <query>${track.data_format.query}</query>
238 </sparql> 252 </sparql>
239 #end if 253 #end if
240 </options> 254 </options>
241 </track> 255 </track>
242 #end if 256 #end if
243 #else if track.data_format.useuri.annouri:
244 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
245 <files>
246 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" label="${track.data_format.useuri.annoname}" useuri="yes">
247 <metadata>
248 <dataset id = "${track.data_format.useuri.annouri}" />
249 </metadata>
250 </trackFile>
251 </files>
252 <options/>
253 </track>
254 #end if 257 #end if
255 #end for 258 #end for
256 #end for 259 #end for
257 </tracks> 260 </tracks>
258 </root> 261 </root>
310 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"/> 313 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"/>
311 <repeat name="data_tracks" title="Annotation Track"> 314 <repeat name="data_tracks" title="Annotation Track">
312 <conditional name="data_format" label="Track Data Selection Options"> 315 <conditional name="data_format" label="Track Data Selection Options">
313 <param type="select" label="Track Type" name="data_format_select"> 316 <param type="select" label="Track Type" name="data_format_select">
314 <option value="bam">BAM Pileup track</option> 317 <option value="bam">BAM Pileup track</option>
318 <option value="bed">BED track</option>
315 <option value="bigwig">BigWig track</option> 319 <option value="bigwig">BigWig track</option>
316 <option value="blastxml">Blast XML track - converted to GFF</option> 320 <option value="blastxml">Blast XML track - converted to GFF</option>
317 <option value="cool">HiC as cool/mcool/scool format files</option> 321 <option value="cool">HiC as cool/mcool/scool format files</option>
318 <option value="cram">CRAM</option> 322 <option value="cram">CRAM</option>
319 <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option> 323 <option value="gff" selected="true">GFF/GFF3 feature track</option>
320 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> 324 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
321 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option> 325 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
322 <option value="paf">PAF - approximate mapping positions between two set of sequences</option> 326 <option value="paf">PAF - approximate mapping positions between two set of sequences</option>
323 <option value="vcf">VCF SNP</option> 327 <option value="vcf">VCF SNP</option>
324 </param> 328 </param>
348 <when value="vcf"> 352 <when value="vcf">
349 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" /> 353 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" />
350 <expand macro="track_styling_vcf"/> 354 <expand macro="track_styling_vcf"/>
351 <expand macro="track_visibility" /> 355 <expand macro="track_visibility" />
352 </when> 356 </when>
353 <when value="gene_calls"> 357 <when value="gff">
354 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" /> 358 <expand macro="input_conditional" label="GFF/GFF3 Track Data" format="gff,gff3" />
355 <conditional name="match_part" label="match/match_part data"> 359 <conditional name="match_part" label="match/match_part data">
356 <param help="Match part data selection " label="This is match/match_part data" name="match_part_select" type="select"> 360 <param help="Match part data selection " label="This is match/match_part data" name="match_part_select" type="select">
357 <option selected="True" value="false">Not match/match part data</option> 361 <option selected="True" value="false">Not match/match part data</option>
358 <option value="true">Match/match part data</option> 362 <option value="true">Match/match part data</option>
359 </param> 363 </param>
369 </conditional> 373 </conditional>
370 <expand macro="track_visibility" /> 374 <expand macro="track_visibility" />
371 </when> 375 </when>
372 <when value="bam"> 376 <when value="bam">
373 <expand macro="input_conditional" label="BAM Track Data" format="bam" /> 377 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
378 <expand macro="track_visibility" />
379 </when>
380 <when value="bed">
381 <expand macro="input_conditional" label="BED Track Data" format="bed" />
374 <expand macro="track_visibility" /> 382 <expand macro="track_visibility" />
375 </when> 383 </when>
376 <when value="cram"> 384 <when value="cram">
377 <expand macro="input_conditional" label="CRAM Track Data" format="cram" /> 385 <expand macro="input_conditional" label="CRAM Track Data" format="cram" />
378 <expand macro="track_visibility" /> 386 <expand macro="track_visibility" />
495 <param name="reference_genome|genome" value="merlin.fa"/> 503 <param name="reference_genome|genome" value="merlin.fa"/>
496 <repeat name="track_groups"> 504 <repeat name="track_groups">
497 <param name="category" value="Default" /> 505 <param name="category" value="Default" />
498 <repeat name="data_tracks"> 506 <repeat name="data_tracks">
499 <conditional name="data_format"> 507 <conditional name="data_format">
500 <param name="data_format_select" value="gene_calls"/> 508 <param name="data_format_select" value="bed"/>
501 <conditional name="useuri"> 509 <conditional name="useuri">
502 <param name="insource" value="history"/> 510 <param name="insource" value="history"/>
503 <param name="annotation" value="bed/test-3.bed"/> 511 <param name="annotation" value="bed/test-3.bed"/>
504 </conditional> 512 </conditional>
505 </conditional> 513 </conditional>
523 <param name="reference_genome|genome" value="merlin.fa"/> 531 <param name="reference_genome|genome" value="merlin.fa"/>
524 <repeat name="track_groups"> 532 <repeat name="track_groups">
525 <param name="category" value="Auto Coloured" /> 533 <param name="category" value="Auto Coloured" />
526 <repeat name="data_tracks"> 534 <repeat name="data_tracks">
527 <conditional name="data_format"> 535 <conditional name="data_format">
528 <param name="data_format_select" value="gene_calls"/> 536 <param name="data_format_select" value="gff"/>
529 <conditional name="useuri"> 537 <conditional name="useuri">
530 <param name="insource" value="history"/> 538 <param name="insource" value="history"/>
531 <param name="annotation" value="gff3/A.gff"/> 539 <param name="annotation" value="gff3/A.gff"/>
532 </conditional> 540 </conditional>
533 <conditional name="match_part"> 541 <conditional name="match_part">
547 555
548 <repeat name="track_groups"> 556 <repeat name="track_groups">
549 <param name="category" value="Ignore Scale" /> 557 <param name="category" value="Ignore Scale" />
550 <repeat name="data_tracks"> 558 <repeat name="data_tracks">
551 <conditional name="data_format"> 559 <conditional name="data_format">
552 <param name="data_format_select" value="gene_calls"/> 560 <param name="data_format_select" value="gff"/>
553 <conditional name="useuri"> 561 <conditional name="useuri">
554 <param name="insource" value="history"/> 562 <param name="insource" value="history"/>
555 <param name="annotation" value="gff3/1.gff"/> 563 <param name="annotation" value="gff3/1.gff"/>
556 </conditional> 564 </conditional>
557 <conditional name="match_part"> 565 <conditional name="match_part">
572 580
573 <repeat name="track_groups"> 581 <repeat name="track_groups">
574 <param name="category" value="Scaled Colour" /> 582 <param name="category" value="Scaled Colour" />
575 <repeat name="data_tracks"> 583 <repeat name="data_tracks">
576 <conditional name="data_format"> 584 <conditional name="data_format">
577 <param name="data_format_select" value="gene_calls"/> 585 <param name="data_format_select" value="gff"/>
578 <conditional name="useuri"> 586 <conditional name="useuri">
579 <param name="insource" value= "history"/> 587 <param name="insource" value= "history"/>
580 <param name="annotation" value="gff3/C.gff"/> 588 <param name="annotation" value="gff3/C.gff"/>
581 </conditional> 589 </conditional>
582 <conditional name="match_part"> 590 <conditional name="match_part">
599 </section> 607 </section>
600 </conditional> 608 </conditional>
601 </repeat> 609 </repeat>
602 <repeat name="data_tracks"> 610 <repeat name="data_tracks">
603 <conditional name="data_format"> 611 <conditional name="data_format">
604 <param name="data_format_select" value="gene_calls"/> 612 <param name="data_format_select" value="gff"/>
605 <conditional name="useuri"> 613 <conditional name="useuri">
606 <param name="annotation" value="gff3/B.gff"/> 614 <param name="annotation" value="gff3/B.gff"/>
607 <param name="insource" value= "history"/> 615 <param name="insource" value= "history"/>
608 </conditional> 616 </conditional>
609 <conditional name="match_part"> 617 <conditional name="match_part">
627 </section> 635 </section>
628 </conditional> 636 </conditional>
629 </repeat> 637 </repeat>
630 <repeat name="data_tracks"> 638 <repeat name="data_tracks">
631 <conditional name="data_format"> 639 <conditional name="data_format">
632 <param name="data_format_select" value="gene_calls"/> 640 <param name="data_format_select" value="gff"/>
633 <conditional name="useuri"> 641 <conditional name="useuri">
634 <param name="annotation" value="gff3/A.gff"/> 642 <param name="annotation" value="gff3/A.gff"/>
635 <param name="insource" value= "history"/> 643 <param name="insource" value= "history"/>
636 </conditional> 644 </conditional>
637 <conditional name="match_part"> 645 <conditional name="match_part">
656 </section> 664 </section>
657 </conditional> 665 </conditional>
658 </repeat> 666 </repeat>
659 <repeat name="data_tracks"> 667 <repeat name="data_tracks">
660 <conditional name="data_format"> 668 <conditional name="data_format">
661 <param name="data_format_select" value="gene_calls"/> 669 <param name="data_format_select" value="gff"/>
662 <conditional name="useuri"> 670 <conditional name="useuri">
663 <param name="annotation" value="gff3/1.gff"/> 671 <param name="annotation" value="gff3/1.gff"/>
664 <param name="insource" value= "history"/> 672 <param name="insource" value= "history"/>
665 </conditional> 673 </conditional>
666 <conditional name="match_part"> 674 <conditional name="match_part">
690 698
691 <repeat name="track_groups"> 699 <repeat name="track_groups">
692 <param name="category" value="Realistic" /> 700 <param name="category" value="Realistic" />
693 <repeat name="data_tracks"> 701 <repeat name="data_tracks">
694 <conditional name="data_format"> 702 <conditional name="data_format">
695 <param name="data_format_select" value="gene_calls"/> 703 <param name="data_format_select" value="gff"/>
696 <conditional name="useuri"> 704 <conditional name="useuri">
697 <param name="annotation" value="gff3/interpro.gff"/> 705 <param name="annotation" value="gff3/interpro.gff"/>
698 <param name="insource" value= "history"/> 706 <param name="insource" value= "history"/>
699 </conditional> 707 </conditional>
700 <conditional name="match_part"> 708 <conditional name="match_part">
710 </section> 718 </section>
711 </conditional> 719 </conditional>
712 </repeat> 720 </repeat>
713 <repeat name="data_tracks"> 721 <repeat name="data_tracks">
714 <conditional name="data_format"> 722 <conditional name="data_format">
715 <param name="data_format_select" value="gene_calls"/> 723 <param name="data_format_select" value="gff"/>
716 <conditional name="useuri"> 724 <conditional name="useuri">
717 <param name="annotation" value="gff3/2.gff"/> 725 <param name="annotation" value="gff3/2.gff"/>
718 <param name="insource" value= "history"/> 726 <param name="insource" value= "history"/>
719 </conditional> 727 </conditional>
720 <conditional name="match_part"> 728 <conditional name="match_part">
753 761
754 <repeat name="track_groups"> 762 <repeat name="track_groups">
755 <param name="category" value="With menu or index" /> 763 <param name="category" value="With menu or index" />
756 <repeat name="data_tracks"> 764 <repeat name="data_tracks">
757 <conditional name="data_format"> 765 <conditional name="data_format">
758 <param name="data_format_select" value="gene_calls"/> 766 <param name="data_format_select" value="gff"/>
759 <conditional name="useuri"> 767 <conditional name="useuri">
760 <param name="annotation" value="gff3/1.gff"/> 768 <param name="annotation" value="gff3/1.gff"/>
761 <param name="insource" value= "history"/> 769 <param name="insource" value= "history"/>
762 </conditional> 770 </conditional>
763 <conditional name="match_part"> 771 <conditional name="match_part">
788 </section> 796 </section>
789 </conditional> 797 </conditional>
790 </repeat> 798 </repeat>
791 <repeat name="data_tracks"> 799 <repeat name="data_tracks">
792 <conditional name="data_format"> 800 <conditional name="data_format">
793 <param name="data_format_select" value="gene_calls"/> 801 <param name="data_format_select" value="gff"/>
794 <conditional name="useuri"> 802 <conditional name="useuri">
795 <param name="annotation" value="gff3/1.gff"/> 803 <param name="annotation" value="gff3/1.gff"/>
796 <param name="insource" value= "history"/> 804 <param name="insource" value= "history"/>
797 </conditional> 805 </conditional>
798 <param name="insource" value= "history"/> 806 <param name="insource" value= "history"/>
813 821
814 <param name="uglyTestingHack" value="enabled" /> 822 <param name="uglyTestingHack" value="enabled" />
815 <output name="output"> 823 <output name="output">
816 <assert_contents> 824 <assert_contents>
817 <has_text text="With menu or index"/> 825 <has_text text="With menu or index"/>
818 <has_text text="gene_calls"/> 826 <has_text text="gff"/>
819 </assert_contents> 827 </assert_contents>
820 </output> 828 </output>
821 </test> 829 </test>
822 <!-- TODO add a synteny test --> 830 <!-- TODO add a synteny test -->
823 <!-- TODO add a bam and a cram test --> 831 <!-- TODO add a bam and a cram test -->