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comparison jbrowse2.xml @ 86:0fae1d68347f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
author fubar
date Wed, 10 Apr 2024 06:08:39 +0000
parents 3b2ff9864995
children de8fb46bc3ef
comparison
equal deleted inserted replaced
85:3b2ff9864995 86:0fae1d68347f
359 <repeat name="track_groups" title="Track Group"> 359 <repeat name="track_groups" title="Track Group">
360 <param label="Track Category" 360 <param label="Track Category"
361 name="category" 361 name="category"
362 type="text" 362 type="text"
363 value="Default" 363 value="Default"
364 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"/> 364 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,
365 which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
365 <repeat name="data_tracks" title="Annotation Track"> 366 <repeat name="data_tracks" title="Annotation Track">
366 <conditional name="data_format" label="Track Data Selection Options"> 367 <conditional name="data_format" label="Track Data Selection Options">
367 <param type="select" label="Track Type" name="data_format_select"> 368 <param type="select" label="Track Type" name="data_format_select">
368 <option value="bam">BAM track. Recommend convert to faster BED unless mapping annotation needed</option> 369 <option value="bam">BAM track. Recommend convert to faster BED unless mapping annotation needed</option>
369 <option value="bed">BED track</option> 370 <option value="bed">BED track</option>
379 </param> 380 </param>
380 <when value="blastxml"> 381 <when value="blastxml">
381 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> 382 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
382 383
383 <param label="Features used in Blast Search" 384 <param label="Features used in Blast Search"
384 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." 385 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
386 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,
387 blastp results on a protein sequence don't need this."
385 format="gff3" 388 format="gff3"
386 name="blast_parent" 389 name="blast_parent"
387 optional="true" 390 optional="true"
388 type="data"/> 391 type="data"/>
389 392
416 <when value="true"> 419 <when value="true">
417 <param label="Match Part Feature Type" 420 <param label="Match Part Feature Type"
418 name="name" 421 name="name"
419 type="text" 422 type="text"
420 value="match" 423 value="match"
421 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)." 424 help="Match_parts have options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc.
425 Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)."
422 optional="True"/> 426 optional="True"/>
423 </when> 427 </when>
424 <when value="false" /> 428 <when value="false" />
425 </conditional> 429 </conditional>
426 <expand macro="track_styling_vgp" /> 430 <expand macro="track_styling_vgp" />
477 <when input="zipOut" value="true" format="zip" /> 481 <when input="zipOut" value="true" format="zip" />
478 </change_format> 482 </change_format>
479 </data> 483 </data>
480 </outputs> 484 </outputs>
481 <tests> 485 <tests>
486 <test>
487 <repeat name="assemblies">
488 <conditional name="reference_genome">
489 <param name="genome_type_select" value="history"/>
490 <param name="genome" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/Merlin" />
491 <param name="genome.ext" value="fasta"/>
492 </conditional>
493 <repeat name="track_groups">
494 <param name="category" value="Assembly properties"/>
495 <repeat name="data_tracks">
496 <conditional name="data_format">
497 <param name="data_format_select" value="gff"/>
498 <conditional name="useuri">
499 <param name="insource" value="history"/>
500 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.gff3"/>
501 </conditional>
502 </conditional>
503 </repeat>
504 <repeat name="data_tracks">
505 <conditional name="data_format">
506 <param name="data_format_select" value="bigwig"/>
507 <conditional name="useuri">
508 <param name="insource" value="history"/>
509 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.bw"/>
510 </conditional>
511 </conditional>
512 </repeat>
513 <repeat name="data_tracks">
514 <conditional name="data_format">
515 <param name="data_format_select" value="bed"/>
516 <conditional name="useuri">
517 <param name="insource" value="history"/>
518 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/test-6.bed"/>
519 </conditional>
520 </conditional>
521 </repeat>
522 <repeat name="data_tracks">
523 <conditional name="data_format">
524 <param name="data_format_select" value="vcf"/>
525 <conditional name="useuri">
526 <param name="insource" value="history"/>
527 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.vcf"/>
528 </conditional>
529 </conditional>
530 </repeat>
531 <repeat name="data_tracks">
532 <conditional name="data_format">
533 <param name="data_format_select" value="cram"/>
534 <conditional name="useuri">
535 <param name="insource" value="history"/>
536 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.cram"/>
537 </conditional>
538 </conditional>
539 </repeat>
540 <repeat name="data_tracks">
541 <conditional name="data_format">
542 <param name="data_format_select" value="bam"/>
543 <conditional name="useuri">
544 <param name="insource" value="history"/>
545 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin-sample.bam"/>
546 </conditional>
547 </conditional>
548 </repeat>
549 <repeat name="data_tracks">
550 <conditional name="data_format">
551 <param name="data_format_select" value="maf"/>
552 <conditional name="useuri">
553 <param name="insource" value="history"/>
554 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlinlastz.maf"/>
555 </conditional>
556 </conditional>
557 </repeat>
558 <repeat name="data_tracks">
559 <conditional name="data_format">
560 <param name="data_format_select" value="blastxml"/>
561 <conditional name="useuri">
562 <param name="insource" value="history"/>
563 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.blastxml"/>
564 </conditional>
565 </conditional>
566 </repeat>
567 </repeat>
568 </repeat>
569 <repeat name="assemblies">
570 <conditional name="reference_genome">
571 <param name="genome_type_select" value="history"/>
572 <param name="genome" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/dm3.fa" />
573 <param name="genome.ext" value="fasta"/>
574 </conditional>
575 <repeat name="track_groups">
576 <param name="category" value="Assembly properties"/>
577 <repeat name="data_tracks">
578 <conditional name="data_format">
579 <param name="data_format_select" value="cool"/>
580 <conditional name="useuri">
581 <param name="insource" value="history"/>
582 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/dm3test.cool"/>
583 </conditional>
584 </conditional>
585 </repeat>
586 </repeat>
587 </repeat>
588 <repeat name="assemblies">
589 <conditional name="reference_genome">
590 <param name="genome_type_select" value="history"/>
591 <param name="genome" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/Ppersica1.fa" />
592 <param name="genome.ext" value="fasta"/>
593 </conditional>
594 <repeat name="track_groups">
595 <param name="category" value="Assembly properties"/>
596 <repeat name="data_tracks">
597 <conditional name="data_format">
598 <param name="data_format_select" value="paf"/>
599 <conditional name="useuri">
600 <param name="insource" value="history"/>
601 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/peach-grape-map.paf"/>
602 </conditional>
603 </conditional>
604
605 <conditional name="pafsuseuri">
606 <conditional name="useuri">
607 <param name="insource" value="history"/>
608 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/Vvinifera1.fa"/>
609 </conditional>
610 </conditional>
611 </repeat>
612 </repeat>
613 </repeat>
614 <repeat name="assemblies">
615 <conditional name="reference_genome">
616 <param name="genome_type_select" value="uri"/>
617 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz" />
618 <param name="refname" value="hg38"/>
619 </conditional>
620 <repeat name="track_groups">
621 <param name="category" value="Assembly properties"/>
622 <repeat name="data_tracks">
623 <conditional name="data_format">
624 <param name="data_format_select" value="hic"/>
625 <conditional name="useuri">
626 <param name="insource" value="uri"/>
627 <param name="annouri" value="https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic"/>
628 <param name="annoname" value="humanhic"/>
629 </conditional>
630 </conditional>
631 </repeat>
632 </repeat>
633 </repeat>
634 <section name="jbgen">
635 <param name="zipOut" value="true" />
636 </section>
637 <output name="output" file="jbrowse2_result02.zip" ftype="zip" compare="sim_size">
638 <assert_contents>
639 <has_archive_member path=".*" n="616" delta="10"/>
640 <has_archive_member path="index.html"/>
641 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
642 <has_archive_member path="manifest.json">
643 <has_text text="favicon.ico"/>
644 <has_text text="background_color"/>
645 </has_archive_member>
646 <has_archive_member path="galaxy.xml">
647 <is_valid_xml />
648 <xml_element path="./metadata/general/session_name" n="1">
649 <has_text_matching expression="New session"/>
650 <not_has_text text="Newton"/>
651 </xml_element>
652 </has_archive_member>
653 <has_archive_member path="merlin.gff3_0.gff3.gz"/>
654 <has_archive_member path="merlin.bw_1.bigwig"/>
655 <has_archive_member path="test-6.bed_2.bed.gz"/>
656 <has_archive_member path="merlin.vcf_3.vcf.tbi"/>
657 <has_archive_member path="merlin.cram_4.cram"/>
658 <has_archive_member path="merlin-sample.bam_5.bam"/>
659 <has_archive_member path="merlinlastz.maf_6.maf.sorted.bed.gz.tbi"/>
660 <has_archive_member path="merlin.blastxml_7.blastxml.gz"/>
661 <has_archive_member path="dm3test.cool_8.cool.hic"/>
662 <has_archive_member path="peach-grape-map.paf_9.paf"/>
663 <has_archive_member path="Merlin.fa.gz.fai"/>
664 <has_archive_member path="config.json">
665 <has_json_property_with_text property="name" text="Merlin" />
666 </has_archive_member>
667
668 </assert_contents>
669 </output>
670 </test>
482 <test> 671 <test>
483 <repeat name="assemblies"> 672 <repeat name="assemblies">
484 <conditional name="reference_genome"> 673 <conditional name="reference_genome">
485 <param name="genome_type_select" value="history"/> 674 <param name="genome_type_select" value="history"/>
486 <param name="genome" value="merlin.fa"/> 675 <param name="genome" value="merlin.fa"/>
832 <has_text text="2.gff"/> 1021 <has_text text="2.gff"/>
833 </assert_contents> 1022 </assert_contents>
834 </output> 1023 </output>
835 </test> 1024 </test>
836 1025
837
838 <!-- TODO add a synteny test --> 1026 <!-- TODO add a synteny test -->
839 <!-- TODO add a bam and a cram test --> 1027 <!-- TODO add a bam and a cram test -->
840 <!-- TODO add an hic test --> 1028 <!-- TODO add an hic test -->
841 <!-- TODO add a vcf_bgzip test --> 1029 <!-- TODO add a vcf_bgzip test -->
842 </tests> 1030 </tests>
895 1083
896 **Track Groups** represent a set of tracks in a single category. 1084 **Track Groups** represent a set of tracks in a single category.
897 1085
898 Annotation Tracks 1086 Annotation Tracks
899 ----------------- 1087 -----------------
1088
1089 MAF
1090 ~~~
1091
1092 For history references, the name of the reference genome dataset in your history is very important for MAF tracks,
1093 because it becomes the "dbkey" for that reference. So, it must be exactly the same as the genome name (dbkey) used
1094 when making the MAF, typically in the Lastz tool.
1095
1096 If you used "hg38" as the reference in Lastz, that is exactly what the reference fasta should be named for any MAF track.
1097 Change it using the "pencil" icon on the reference data in your history. Any other name, such as "hg38.fasta"
1098 will cause the MAF track to show no data since there are no matches with that reference dbkey.
1099
900 1100
901 GFF3/BED 1101 GFF3/BED
902 ~~~~~~~~ 1102 ~~~~~~~~
903 1103
904 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region. 1104 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region.