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comparison jbrowse2.xml @ 97:74074746ccd8 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
author fubar
date Sat, 01 Jun 2024 05:37:13 +0000
parents 4c517a0041a8
children b1260bca5fdc
comparison
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96:5ef1ba2031f2 97:74074746ccd8
1 <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_17" profile="22.05"> 1 <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_17" profile="22.05">
2 <description>genome browser</description> 2 <description>genome browser</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edamInc" /> 6 <expand macro="edamInc"/>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">jbrowse2</xref> 8 <xref type="bio.tools">jbrowse2</xref>
9 </xrefs> 9 </xrefs>
10 <expand macro="requirements" /> 10 <expand macro="requirements" />
11 <expand macro="creators"/>
11 <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command> 12 <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command>
13 <required_files>
14 <include path="autogenJB2.py" />
15 <include path="blastxml_to_gapped_gff3.py" />
16 <include path="convertMAF.sh" />
17 <include path="gff3_rebase.py" />
18 <include path="jb2_urlconf.py" />
19 <include path="jb2_webserver.py" />
20 <include path="jbrowse2.py" />
21 <include path="maf2bed.py" />
22 </required_files>
12 <command detect_errors="aggressive"><![CDATA[ 23 <command detect_errors="aggressive"><![CDATA[
13 mkdir -p '$output.files_path' && 24 mkdir -p '$output.files_path' &&
14 cp '$trackxml' '$output.files_path/galaxy.xml' && 25 cp '$trackxml' '$output.files_path/galaxy.xml' &&
15 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && 26 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
16 #if $jbgen.ucol.formcoll=="collect": 27 #if $jbgen.ucol.formcoll=="collect":
17 python '$__tool_directory__/autogenJB2.py' 28 python '$__tool_directory__/autogenJB2.py'
18 #for $key in $autoCollection.keys(): 29 #for $key in $autoCollection.keys():
19 #if $autoCollection[$key].is_collection: 30 #if $autoCollection[$key].is_collection:
20 #set subCol=$autoCollection[$key] 31 #set subCol=$autoCollection[$key]
21 #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf'] 32 #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf']
33 #set refs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext in ['fasta.gz','fasta']]
22 #if len($pafs) > 0: 34 #if len($pafs) > 0:
23 --pafmeta '$pafs[0]' 35 --pafmeta '$pafs[0]'
24 #set refs = [($pafs[0][2],$subCol[x],x) for x in $subCol.keys() if $subCol[x].ext == 'fasta']
25 #for $ref in $refs: 36 #for $ref in $refs:
26 --pafreferencemeta '$ref' 37 --pafreferencemeta '$ref'
27 #end for 38 #end for
28 #end if 39 #end if
29 #else if $autoCollection[$key].ext == 'fasta': 40 #else if $autoCollection[$key].ext == 'fasta':
308 #end if 319 #end if
309 </root> 320 </root>
310 ]]></configfile> 321 ]]></configfile>
311 </configfiles> 322 </configfiles>
312 <inputs> 323 <inputs>
313 <repeat name="assemblies" min="1" 324 <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">
314 title="Genome reference to provide display coordinates for this set of tracks"
315 help="JBrowse2 can show a set of tracks for each of multiple genome reference fasta files">
316 <conditional name="reference_genome"> 325 <conditional name="reference_genome">
317 <param help="Select a built in, history or remote tabix URI for the reference track" 326 <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">
318 label="Reference genome source" name="genome_type_select" type="select">
319 <option selected="True" value="indexed">Use a Galaxy server built-in genome</option> 327 <option selected="True" value="indexed">Use a Galaxy server built-in genome</option>
320 <option value="history">Use a genome fasta file from the current history</option> 328 <option value="history">Use a genome fasta file from the current history</option>
321 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as 329 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as
322 tabix bgzip with predictable index file URI</option> 330 tabix bgzip with predictable index file URI</option>
323 </param> 331 </param>
324 <when value="indexed"> 332 <when value="indexed">
325 <param 333 <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">
326 help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome"
327 label="Select a built in reference genome or custom genome"
328 name="genome"
329 type="select"
330 optional="true">
331 <options from_data_table="all_fasta"> 334 <options from_data_table="all_fasta">
332 <filter column="2" type="sort_by" /> 335 <filter column="2" type="sort_by"/>
333 <validator 336 <validator message="No genomes are available for the selected input dataset" type="no_options">
334 message="No genomes are available for the selected input dataset"
335 type="no_options">
336 </validator> 337 </validator>
337 </options> 338 </options>
338 </param> 339 </param>
339 </when> 340 </when>
340 <when value="history"> 341 <when value="history">
341 <param 342 <param name="genome" type="data" format="fasta" optional="true" label="Select the reference genome">
342 format="fasta"
343 label="Select the reference genome"
344 name="genome"
345 type="data"
346 optional="true">
347 </param> 343 </param>
348 </when> 344 </when>
349 <when value="uri"> 345 <when value="uri">
350 <param 346 <param name="uri" type="text" label="URI pointing to tabix compressed fasta">
351 label="URI pointing to tabix compressed fasta"
352 name="uri"
353 type="text">
354 </param> 347 </param>
355 <param 348 <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4">
356 label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"
357 name="refname"
358 type="text">
359 </param> 349 </param>
360 </when> 350 </when>
361 </conditional> 351 </conditional>
362
363 <repeat name="track_groups" title="Track Group"> 352 <repeat name="track_groups" title="Track Group">
364 <param label="Track Category" 353 <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."/>
365 name="category"
366 type="text"
367 value="Default"
368 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,
369 which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated."
370 optional="False" />
371 <repeat name="data_tracks" title="Annotation Track"> 354 <repeat name="data_tracks" title="Annotation Track">
372 <conditional name="data_format" label="Track Data Selection Options"> 355 <conditional name="data_format" label="Track Data Selection Options">
373 <param type="select" label="Track Type" name="data_format_select"> 356 <param name="data_format_select" type="select" label="Track Type">
374 <option value="bam">BAM track. Recommend convert to faster BED unless 357 <option value="bam">BAM track. Recommend convert to faster BED unless
375 mapping annotation needed</option> 358 mapping annotation needed</option>
376 <option value="bed">BED track</option> 359 <option value="bed">BED track</option>
377 <option value="bigwig">BigWig track</option> 360 <option value="bigwig">BigWig track</option>
378 <option value="blastxml">Blast XML track (as GFF3)</option> 361 <option value="blastxml">Blast XML track (as GFF3)</option>
387 <option value="paf">PAF - approximate mapping positions between two set 370 <option value="paf">PAF - approximate mapping positions between two set
388 of sequences</option> 371 of sequences</option>
389 <option value="vcf">VCF SNP track</option> 372 <option value="vcf">VCF SNP track</option>
390 </param> 373 </param>
391 <when value="blastxml"> 374 <when value="blastxml">
392 <expand macro="input_conditional" label="BlastXML Track Data" 375 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml"/>
393 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."/>
394 <param label="Features used in Blast Search" 377 <param name="min_gap" type="integer" min="2" value="10" label="Minimum Gap Size" help="before a new match_part feature is created"/>
395 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 378 <param name="is_protein" type="boolean" truevalue="true" falsevalue="false" label="Is this a protein blast search?"/>
396 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, 379 <expand macro="track_styling_vgp"/>
397 blastp results on a protein sequence don't need this." 380 <expand macro="track_visibility"/>
398 format="gff3"
399 name="blast_parent"
400 optional="true"
401 type="data" />
402 <param label="Minimum Gap Size"
403 help="before a new match_part feature is created"
404 name="min_gap"
405 type="integer"
406 value="10"
407 min="2" />
408 <param label="Is this a protein blast search?"
409 type="boolean"
410 name="is_protein"
411 truevalue="true"
412 falsevalue="false" />
413 <expand macro="track_styling_vgp" />
414 <expand macro="track_visibility" />
415 </when> 381 </when>
416 <when value="vcf"> 382 <when value="vcf">
417 <expand macro="input_conditional" label="SNP Track Data" 383 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip"/>
418 format="vcf,vcf_bgzip" /> 384 <expand macro="track_styling_vcf"/>
419 <expand macro="track_styling_vcf" /> 385 <expand macro="track_visibility"/>
420 <expand macro="track_visibility" />
421 </when> 386 </when>
422 <when value="gff"> 387 <when value="gff">
423 <expand macro="input_conditional" label="GFF/GFF3 Track Data" 388 <expand macro="input_conditional" label="GFF/GFF3 Track Data" format="gff,gff3"/>
424 format="gff,gff3" />
425 <conditional name="match_part" label="match/match_part data"> 389 <conditional name="match_part" label="match/match_part data">
426 <param help="Match part data selection " 390 <param name="match_part_select" type="select" label="This is match/match_part data" help="Match part data selection ">
427 label="This is match/match_part data" name="match_part_select"
428 type="select">
429 <option selected="True" value="false">Not match/match part data</option> 391 <option selected="True" value="false">Not match/match part data</option>
430 <option value="true">Match/match part data</option> 392 <option value="true">Match/match part data</option>
431 </param> 393 </param>
432 <when value="true"> 394 <when value="true">
433 <param label="Match Part Feature Type" 395 <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)."/>
434 name="name"
435 type="text"
436 value="match"
437 help="Match_parts have options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc.
438 Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)."
439 optional="True" />
440 </when> 396 </when>
441 <when value="false" /> 397 <when value="false"/>
442 </conditional> 398 </conditional>
443 <expand macro="track_styling_vgp" /> 399 <expand macro="track_styling_vgp"/>
444 <expand macro="track_visibility" /> 400 <expand macro="track_visibility"/>
445 </when> 401 </when>
446 <when value="bam"> 402 <when value="bam">
447 <expand macro="input_conditional" label="BAM Track Data" format="bam" /> 403 <expand macro="input_conditional" label="BAM Track Data" format="bam"/>
448 <expand macro="track_visibility" /> 404 <expand macro="track_visibility"/>
449 </when> 405 </when>
450 <when value="bed"> 406 <when value="bed">
451 <expand macro="input_conditional" label="BED Track Data" format="bed" /> 407 <expand macro="input_conditional" label="BED Track Data" format="bed"/>
452 <expand macro="track_styling_vgp" /> 408 <expand macro="track_styling_vgp"/>
453 <expand macro="track_visibility" /> 409 <expand macro="track_visibility"/>
454 </when> 410 </when>
455 <when value="cram"> 411 <when value="cram">
456 <expand macro="input_conditional" label="CRAM Track Data" format="cram" /> 412 <expand macro="input_conditional" label="CRAM Track Data" format="cram"/>
457 <expand macro="track_visibility" /> 413 <expand macro="track_visibility"/>
458 </when> 414 </when>
459 <when value="maf"> 415 <when value="maf">
460 <expand macro="input_conditional" label="MAF Track Data" format="maf" /> 416 <expand macro="input_conditional" label="MAF Track Data" format="maf"/>
461 <expand macro="track_styling_vgp" /> 417 <expand macro="track_styling_vgp"/>
462 <expand macro="track_visibility" /> 418 <expand macro="track_visibility"/>
463 </when> 419 </when>
464 <when value="bigwig"> 420 <when value="bigwig">
465 <expand macro="input_conditional" label="BigWig Track Data" 421 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig"/>
466 format="bigwig" /> 422 <expand macro="track_visibility"/>
467 <expand macro="track_visibility" />
468 </when> 423 </when>
469 <when value="paf"> 424 <when value="paf">
470 <expand macro="input_conditional" 425 <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"/>
471 label="PAF format synteny mapping data" format="paf" 426 <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"/>
472 help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references" /> 427 <expand macro="track_visibility"/>
473 <expand macro="pafref_conditional" label="Comparison genome sequence(s)"
474 format="fasta"
475 help="Paf from these as the reference(s), using the common reference as the reads to map" />
476 <expand macro="track_visibility" />
477 </when> 428 </when>
478 <when value="hic"> 429 <when value="hic">
479 <expand macro="input_conditional" label="Binary Juicebox HiC data" 430 <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic"/>
480 format="hic,juicebox_hic" /> 431 <expand macro="track_visibility"/>
481 <expand macro="track_visibility" />
482 </when> 432 </when>
483 <when value="cool"> 433 <when value="cool">
484 <expand macro="input_conditional" 434 <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool"/>
485 label="HiC data in cool/mcool/scool format" 435 <expand macro="track_visibility"/>
486 format="cool,mcool,scool" />
487 <expand macro="track_visibility" />
488 </when> 436 </when>
489 </conditional> 437 </conditional>
490 </repeat> 438 </repeat>
491 </repeat> 439 </repeat>
492 </repeat> 440 </repeat>
493 <expand macro="general_options" /> 441 <expand macro="general_options"/>
494 <param type="hidden" name="uglyTestingHack" value="" /> 442 <param name="uglyTestingHack" type="hidden" value=""/>
495 </inputs> 443 </inputs>
496 <outputs> 444 <outputs>
497 <data format="html" name="output" label="JBrowse2: ${jbgen.session_name}"> 445 <data format="html" name="output" label="JBrowse2: ${jbgen.session_name}">
498 <change_format> 446 <change_format>
499 <when input="zipOut" value="true" format="zip" /> 447 <when input="zipOut" value="true" format="zip"/>
500 </change_format> 448 </change_format>
501 </data> 449 </data>
502 </outputs> 450 </outputs>
503 <tests> 451 <tests>
504 <test> 452 <test>
505 <repeat name="assemblies"> 453 <repeat name="assemblies">
506 <conditional name="reference_genome"> 454 <conditional name="reference_genome">
507 <param name="genome_type_select" value="history" /> 455 <param name="genome_type_select" value="history"/>
508 <param name="genome" 456 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Merlin"/>
509 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/Merlin" /> 457 <param name="genome.ext" value="fasta"/>
510 <param name="genome.ext" value="fasta" />
511 </conditional> 458 </conditional>
512 <repeat name="track_groups"> 459 <repeat name="track_groups">
513 <param name="category" value="Assembly properties" /> 460 <param name="category" value="Assembly properties"/>
514 <repeat name="data_tracks"> 461 <repeat name="data_tracks">
515 <conditional name="data_format"> 462 <conditional name="data_format">
516 <param name="data_format_select" value="gff" /> 463 <param name="data_format_select" value="gff"/>
517 <conditional name="useuri"> 464 <conditional name="useuri">
518 <param name="insource" value="history" /> 465 <param name="insource" value="history"/>
519 <param name="annotation" 466 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.gff3"/>
520 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.gff3" /> 467 </conditional>
521 </conditional> 468 </conditional>
522 </conditional> 469 </repeat>
523 </repeat> 470 <repeat name="data_tracks">
524 <repeat name="data_tracks"> 471 <conditional name="data_format">
525 <conditional name="data_format"> 472 <param name="data_format_select" value="bigwig"/>
526 <param name="data_format_select" value="bigwig" /> 473 <conditional name="useuri">
527 <conditional name="useuri"> 474 <param name="insource" value="history"/>
528 <param name="insource" value="history" /> 475 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.bw"/>
529 <param name="annotation" 476 </conditional>
530 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.bw" /> 477 </conditional>
531 </conditional> 478 </repeat>
532 </conditional> 479 <repeat name="data_tracks">
533 </repeat> 480 <conditional name="data_format">
534 <repeat name="data_tracks"> 481 <param name="data_format_select" value="bed"/>
535 <conditional name="data_format"> 482 <conditional name="useuri">
536 <param name="data_format_select" value="bed" /> 483 <param name="insource" value="history"/>
537 <conditional name="useuri"> 484 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/test-6.bed"/>
538 <param name="insource" value="history" /> 485 </conditional>
539 <param name="annotation" 486 </conditional>
540 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/test-6.bed" /> 487 </repeat>
541 </conditional> 488 <repeat name="data_tracks">
542 </conditional> 489 <conditional name="data_format">
543 </repeat> 490 <param name="data_format_select" value="vcf"/>
544 <repeat name="data_tracks"> 491 <conditional name="useuri">
545 <conditional name="data_format"> 492 <param name="insource" value="history"/>
546 <param name="data_format_select" value="vcf" /> 493 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.vcf"/>
547 <conditional name="useuri"> 494 </conditional>
548 <param name="insource" value="history" /> 495 </conditional>
549 <param name="annotation" 496 </repeat>
550 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.vcf" /> 497 <repeat name="data_tracks">
551 </conditional> 498 <conditional name="data_format">
552 </conditional> 499 <param name="data_format_select" value="cram"/>
553 </repeat> 500 <conditional name="useuri">
554 <repeat name="data_tracks"> 501 <param name="insource" value="history"/>
555 <conditional name="data_format"> 502 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.cram"/>
556 <param name="data_format_select" value="cram" /> 503 </conditional>
557 <conditional name="useuri"> 504 </conditional>
558 <param name="insource" value="history" /> 505 </repeat>
559 <param name="annotation" 506 <repeat name="data_tracks">
560 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.cram" /> 507 <conditional name="data_format">
561 </conditional> 508 <param name="data_format_select" value="bam"/>
562 </conditional> 509 <conditional name="useuri">
563 </repeat> 510 <param name="insource" value="history"/>
564 <repeat name="data_tracks"> 511 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin-sample.bam"/>
565 <conditional name="data_format"> 512 </conditional>
566 <param name="data_format_select" value="bam" /> 513 </conditional>
567 <conditional name="useuri"> 514 </repeat>
568 <param name="insource" value="history" /> 515 <repeat name="data_tracks">
569 <param name="annotation" 516 <conditional name="data_format">
570 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin-sample.bam" /> 517 <param name="data_format_select" value="maf"/>
571 </conditional> 518 <conditional name="useuri">
572 </conditional> 519 <param name="insource" value="history"/>
573 </repeat> 520 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlinlastz.maf"/>
574 <repeat name="data_tracks"> 521 </conditional>
575 <conditional name="data_format"> 522 </conditional>
576 <param name="data_format_select" value="maf" /> 523 </repeat>
577 <conditional name="useuri"> 524 <repeat name="data_tracks">
578 <param name="insource" value="history" /> 525 <conditional name="data_format">
579 <param name="annotation" 526 <param name="data_format_select" value="blastxml"/>
580 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlinlastz.maf" /> 527 <conditional name="useuri">
581 </conditional> 528 <param name="insource" value="history"/>
582 </conditional> 529 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.blastxml"/>
583 </repeat> 530 </conditional>
584 <repeat name="data_tracks"> 531 </conditional>
585 <conditional name="data_format"> 532 </repeat>
586 <param name="data_format_select" value="blastxml" /> 533 <repeat name="data_tracks">
587 <conditional name="useuri"> 534 <conditional name="data_format">
588 <param name="insource" value="history" /> 535 <param name="data_format_select" value="bam"/>
589 <param name="annotation" 536 <conditional name="useuri">
590 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.blastxml" /> 537 <param name="insource" value="history"/>
591 </conditional> 538 <param name="annotation" value=""/>
592 </conditional>
593 </repeat>
594 <repeat name="data_tracks">
595 <conditional name="data_format">
596 <param name="data_format_select" value="bam" />
597 <conditional name="useuri">
598 <param name="insource" value="history" />
599 <param name="annotation" value="" />
600 </conditional> 539 </conditional>
601 </conditional> 540 </conditional>
602 </repeat> 541 </repeat>
603 </repeat> 542 </repeat>
604 </repeat> 543 </repeat>
605 <repeat name="assemblies"> 544 <repeat name="assemblies">
606 <conditional name="reference_genome"> 545 <conditional name="reference_genome">
607 <param name="genome_type_select" value="history" /> 546 <param name="genome_type_select" value="history"/>
608 <param name="genome" 547 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/dm3.fa"/>
609 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/dm3.fa" /> 548 <param name="genome.ext" value="fasta"/>
610 <param name="genome.ext" value="fasta" />
611 </conditional> 549 </conditional>
612 <repeat name="track_groups"> 550 <repeat name="track_groups">
613 <param name="category" value="Assembly properties" /> 551 <param name="category" value="Assembly properties"/>
614 <repeat name="data_tracks"> 552 <repeat name="data_tracks">
615 <conditional name="data_format"> 553 <conditional name="data_format">
616 <param name="data_format_select" value="cool" /> 554 <param name="data_format_select" value="cool"/>
617 <conditional name="useuri"> 555 <conditional name="useuri">
618 <param name="insource" value="history" /> 556 <param name="insource" value="history"/>
619 <param name="annotation" 557 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/dm3test.cool"/>
620 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/dm3test.cool" />
621 </conditional> 558 </conditional>
622 </conditional> 559 </conditional>
623 </repeat> 560 </repeat>
624 </repeat> 561 </repeat>
625 </repeat> 562 </repeat>
626 <repeat name="assemblies"> 563 <repeat name="assemblies">
627 <conditional name="reference_genome"> 564 <conditional name="reference_genome">
628 <param name="genome_type_select" value="history" /> 565 <param name="genome_type_select" value="history"/>
629 <param name="genome" 566 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Ppersica1.fa"/>
630 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/Ppersica1.fa" /> 567 <param name="genome.ext" value="fasta"/>
631 <param name="genome.ext" value="fasta" />
632 </conditional> 568 </conditional>
633 <repeat name="track_groups"> 569 <repeat name="track_groups">
634 <param name="category" value="Assembly properties" /> 570 <param name="category" value="Assembly properties"/>
635 <repeat name="data_tracks"> 571 <repeat name="data_tracks">
636 <conditional name="data_format"> 572 <conditional name="data_format">
637 <param name="data_format_select" value="paf" /> 573 <param name="data_format_select" value="paf"/>
638 <conditional name="useuri"> 574 <conditional name="useuri">
639 <param name="insource" value="history" /> 575 <param name="insource" value="history"/>
640 <param name="annotation" 576 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/peach-grape-map.paf"/>
641 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/peach-grape-map.paf" />
642 </conditional> 577 </conditional>
643 <conditional name="pafuseuri"> 578 <conditional name="pafuseuri">
644 <param name="insource" value="history" /> 579 <param name="insource" value="history"/>
645 <param name="annotation" 580 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa"/>
646 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/Vvinifera1.fa" /> 581 </conditional>
647 </conditional> 582 </conditional>
648 </conditional> 583 </repeat>
649 </repeat> 584 <repeat name="data_tracks">
650 <repeat name="data_tracks"> 585 <conditional name="data_format">
651 <conditional name="data_format"> 586 <param name="data_format_select" value="paf"/>
652 <param name="data_format_select" value="paf" /> 587 <conditional name="useuri">
653 <conditional name="useuri"> 588 <param name="insource" value="history"/>
654 <param name="insource" value="history" /> 589 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabgrapepeach.paf"/>
655 <param name="annotation"
656 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/arabgrapepeach.paf" />
657 </conditional> 590 </conditional>
658 <conditional name="pafuseuri"> 591 <conditional name="pafuseuri">
659 <param name="insource" value="uri" /> 592 <param name="insource" value="uri"/>
660 <repeat name="refuri"> 593 <repeat name="refuri">
661 <param name="annotation" 594 <param name="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz"/>
662 value="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/arabidopsis.fa.gz" /> 595 <param name="annoname" value="arabidopsis.URI"/>
663 <param name="annoname" value="arabidopsis.URI" />
664 </repeat> 596 </repeat>
665 <repeat name="refuri"> 597 <repeat name="refuri">
666 <param name="annotation" 598 <param name="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz"/>
667 value="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/Vvinifera1.fa.gz" /> 599 <param name="annoname" value="Vvinifera1.URI"/>
668 <param name="annoname" value="Vvinifera1.URI" />
669 </repeat> 600 </repeat>
670 </conditional> 601 </conditional>
671 </conditional> 602 </conditional>
672 </repeat> 603 </repeat>
673 <repeat name="data_tracks"> 604 <repeat name="data_tracks">
674 <conditional name="data_format"> 605 <conditional name="data_format">
675 <param name="data_format_select" value="paf" /> 606 <param name="data_format_select" value="paf"/>
676 <conditional name="useuri"> 607 <conditional name="useuri">
677 <param name="insource" value="history" /> 608 <param name="insource" value="history"/>
678 <param name="annotation" 609 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabgrapepeach.paf"/>
679 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/arabgrapepeach.paf" />
680 </conditional> 610 </conditional>
681 <conditional name="pafuseuri"> 611 <conditional name="pafuseuri">
682 <param name="insource" value="history" /> 612 <param name="insource" value="history"/>
683 <param name="annotation" 613 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa"/>
684 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/arabidopsis.fa" /> 614 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa"/>
685 <param name="annotation"
686 location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/Vvinifera1.fa" />
687 </conditional> 615 </conditional>
688 </conditional> 616 </conditional>
689 </repeat> 617 </repeat>
690 </repeat> 618 </repeat>
691 </repeat> 619 </repeat>
692 <repeat name="assemblies"> 620 <repeat name="assemblies">
693 <conditional name="reference_genome"> 621 <conditional name="reference_genome">
694 <param name="genome_type_select" value="uri" /> 622 <param name="genome_type_select" value="uri"/>
695 <param name="uri" 623 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz"/>
696 value="https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz" /> 624 <param name="refname" value="hg38"/>
697 <param name="refname" value="hg38" />
698 </conditional> 625 </conditional>
699 <repeat name="track_groups"> 626 <repeat name="track_groups">
700 <param name="category" value="Assembly properties" /> 627 <param name="category" value="Assembly properties"/>
701 <repeat name="data_tracks"> 628 <repeat name="data_tracks">
702 <conditional name="data_format"> 629 <conditional name="data_format">
703 <param name="data_format_select" value="hic" /> 630 <param name="data_format_select" value="hic"/>
704 <conditional name="useuri"> 631 <conditional name="useuri">
705 <param name="insource" value="uri" /> 632 <param name="insource" value="uri"/>
706 <param name="annouri" 633 <param name="annouri" value="https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic"/>
707 value="https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic" /> 634 <param name="annoname" value="humanhic"/>
708 <param name="annoname" value="humanhic" />
709 </conditional> 635 </conditional>
710 </conditional> 636 </conditional>
711 </repeat> 637 </repeat>
712 </repeat> 638 </repeat>
713 </repeat> 639 </repeat>
714 <section name="jbgen"> 640 <section name="jbgen">
715 <param name="zipOut" value="true" /> 641 <param name="zipOut" value="true"/>
716 <param name="session_name" value="New test session" /> 642 <param name="session_name" value="New test session"/>
717 </section> 643 </section>
718 <output name="output" file="jbrowse2_result02.zip" ftype="zip" compare="sim_size"> 644 <!-- use the following line to generate a ZIP file to inspect it -->
645 <!--output name="output" file="jbrowse2_result02.zip" ftype="zip" compare="sim_size"-->
646 <output name="output" ftype="zip">
719 <assert_contents> 647 <assert_contents>
720 <has_archive_member path=".*" n="637" delta="10" /> 648 <has_archive_member path=".*" n="637" delta="10"/>
721 <has_archive_member path="index.html" /> 649 <has_archive_member path="index.html"/>
722 <has_archive_member 650 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
723 path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff" />
724 <has_archive_member path="manifest.json"> 651 <has_archive_member path="manifest.json">
725 <has_text text="favicon.ico" /> 652 <has_text text="favicon.ico"/>
726 <has_text text="background_color" /> 653 <has_text text="background_color"/>
727 </has_archive_member> 654 </has_archive_member>
728 <has_archive_member path="galaxy.xml"> 655 <has_archive_member path="galaxy.xml">
729 <is_valid_xml /> 656 <is_valid_xml/>
730 <xml_element path="./metadata/general/session_name" n="1"> 657 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/>
731 <has_text_matching expression="New test session" /> 658 <element_text_is path="./metadata/general/session_name" text="New test session"/>
732 <not_has_text text="Newton" />
733 </xml_element>
734 </has_archive_member> 659 </has_archive_member>
735 <has_archive_member path="merlin.gff3_0.gz" /> 660 <has_archive_member path="merlin.gff3_0.gz"/>
736 <has_archive_member path="merlin.gff3_0.gz.tbi" /> 661 <has_archive_member path="merlin.gff3_0.gz.tbi"/>
737 <has_archive_member path="merlin.bw_1" /> 662 <has_archive_member path="merlin.bw_1"/>
738 <has_archive_member path="test-6.bed_2.gz" /> 663 <has_archive_member path="test-6.bed_2.gz"/>
739 <has_archive_member path="merlin.vcf_3" /> 664 <has_archive_member path="merlin.vcf_3"/>
740 <has_archive_member path="merlin.vcf_3.tbi" /> 665 <has_archive_member path="merlin.vcf_3.tbi"/>
741 <has_archive_member path="merlin.cram_4" /> 666 <has_archive_member path="merlin.cram_4"/>
742 <has_archive_member path="merlin.cram_4.crai" /> 667 <has_archive_member path="merlin.cram_4.crai"/>
743 <has_archive_member path="merlin-sample.bam_5" /> 668 <has_archive_member path="merlin-sample.bam_5"/>
744 <has_archive_member path="merlin-sample.bam_5.bai" /> 669 <has_archive_member path="merlin-sample.bam_5.bai"/>
745 <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi" /> 670 <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi"/>
746 <has_archive_member path="merlin.blastxml_7.gz" /> 671 <has_archive_member path="merlin.blastxml_7.gz"/>
747 <has_archive_member path="dm3test.cool_9.hic" /> 672 <has_archive_member path="dm3test.cool_9.hic"/>
748 <has_archive_member path="peach-grape-map.paf_10" /> 673 <has_archive_member path="peach-grape-map.paf_10"/>
749 <has_archive_member path="arabgrapepeach.paf_11" /> 674 <has_archive_member path="arabgrapepeach.paf_11"/>
750 <has_archive_member path="Merlin.fa.gz.fai" /> 675 <has_archive_member path="Merlin.fa.gz.fai"/>
751 <has_archive_member path="dm3.fa.fa.gz.fai" /> 676 <has_archive_member path="dm3.fa.fa.gz.fai"/>
752 <has_archive_member path="Ppersica1.fa.fa.gz" /> 677 <has_archive_member path="Ppersica1.fa.fa.gz"/>
753 <has_archive_member path="Ppersica1.fa.fa.gz.fai" /> 678 <has_archive_member path="Ppersica1.fa.fa.gz.fai"/>
754 <has_archive_member path="Ppersica1.fa.fa.gz.gzi" /> 679 <has_archive_member path="Ppersica1.fa.fa.gz.gzi"/>
755 <has_archive_member path="Vvinifera1.fa.fa.gz.fai" /> 680 <has_archive_member path="Vvinifera1.fa.fa.gz.fai"/>
756 <has_archive_member path="Vvinifera1.fa.fa.gz" /> 681 <has_archive_member path="Vvinifera1.fa.fa.gz"/>
757 <has_archive_member path="Vvinifera1.fa.fa.gz.gzi" /> 682 <has_archive_member path="Vvinifera1.fa.fa.gz.gzi"/>
758 <has_archive_member path="config.json"> 683 <has_archive_member path="config.json">
759 <has_json_property_with_text property="name" text="Merlin" /> 684 <has_json_property_with_text property="name" text="Merlin"/>
760 </has_archive_member> 685 </has_archive_member>
761 </assert_contents> 686 </assert_contents>
762 </output> 687 </output>
763 </test> 688 </test>
764 <test> 689 <test>
765 <param name="autoCollection"> 690 <param name="autoCollection">
766 <collection type="list" name="merlintest"> 691 <collection type="list" name="merlintest">
767 <element name="merlin.fa" value="merlin.fa" /> 692 <element name="merlin.fa" value="merlin.fa"/>
768 <element name="merlin.bw" value="bw/merlin.bw" /> 693 <element name="merlin.bw" value="bw/merlin.bw"/>
769 <element name="test-6.bed" value="bed/test-6.bed" /> 694 <element name="test-6.bed" value="bed/test-6.bed"/>
770 </collection> 695 </collection>
771 </param> 696 </param>
772 <section name="jbgen"> 697 <section name="jbgen">
773 <param name="zipOut" value="true" /> 698 <param name="zipOut" value="true"/>
774 <param name="session_name" value="Collection test" /> 699 <param name="session_name" value="Collection test"/>
775 <param name="ucol|formcoll" value="collect" /> 700 <param name="ucol|formcoll" value="collect"/>
776 </section> 701 </section>
777 <output name="output" file="jbrowse2_result01.zip" ftype="zip" compare="sim_size"> 702 <!-- use the following line to generate a ZIP file to inspect it -->
703 <!--output name="output" file="jbrowse2_result01.zip" ftype="zip" compare="sim_size"-->
704 <output name="output" ftype="zip">
778 <assert_contents> 705 <assert_contents>
779 <has_archive_member path=".*" n="611" delta="10" /> 706 <has_archive_member path=".*" n="611" delta="10"/>
780 <has_archive_member path="index.html" /> 707 <has_archive_member path="index.html"/>
781 <has_archive_member 708 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
782 path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff" />
783 <has_archive_member path="manifest.json"> 709 <has_archive_member path="manifest.json">
784 <has_text text="favicon.ico" /> 710 <has_text text="favicon.ico"/>
785 <has_text text="background_color" /> 711 <has_text text="background_color"/>
786 </has_archive_member> 712 </has_archive_member>
787 <has_archive_member path="galaxy.xml"> 713 <has_archive_member path="galaxy.xml">
788 <is_valid_xml /> 714 <is_valid_xml/>
789 <xml_element path="./metadata/general/session_name" n="1"> 715 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/>
790 <has_text_matching expression="Collection test" /> 716 <element_text_is path="./metadata/general/session_name" text="Collection test"/>
791 <not_has_text text="Newton" />
792 </xml_element>
793 </has_archive_member> 717 </has_archive_member>
794 <has_archive_member path="jb2_webserver.py" /> 718 <has_archive_member path="jb2_webserver.py"/>
795 <has_archive_member path="merlin.fa.fa.gz.gzi"/> 719 <has_archive_member path="merlin.fa.fa.gz.gzi"/>
796 <has_archive_member path="merlin.fa.fa.gz"/> 720 <has_archive_member path="merlin.fa.fa.gz"/>
797 <has_archive_member path="merlin.fa.fa.gz.fai"/> 721 <has_archive_member path="merlin.fa.fa.gz.fai"/>
798 <has_archive_member path="merlin.bw" /> 722 <has_archive_member path="merlin.bw"/>
799 <has_archive_member path="index.html" /> 723 <has_archive_member path="index.html"/>
800 <has_archive_member path="test-6.bed.gz"/> 724 <has_archive_member path="test-6.bed.gz"/>
801 <has_archive_member path="test-6.bed.gz.tbi"/> 725 <has_archive_member path="test-6.bed.gz.tbi"/>
802 </assert_contents> 726 </assert_contents>
803 </output> 727 </output>
804 </test> 728 </test>
805 <test> 729 <test>
806 <repeat name="assemblies"> 730 <repeat name="assemblies">
807 <conditional name="reference_genome"> 731 <conditional name="reference_genome">
808 <param name="genome_type_select" value="history" /> 732 <param name="genome_type_select" value="history"/>
809 <param name="genome" value="merlin.fa" /> 733 <param name="genome" value="merlin.fa"/>
810 <param name="genome.ext" value="fasta" /> 734 <param name="genome.ext" value="fasta"/>
811 <param name="genome.name" value="Merlin" /> 735 <param name="genome.name" value="Merlin"/>
812 </conditional> 736 </conditional>
813 <repeat name="track_groups"> 737 <repeat name="track_groups">
814 <param name="category" value="Default" /> 738 <param name="category" value="Default"/>
815 <repeat name="data_tracks"> 739 <repeat name="data_tracks">
816 <conditional name="data_format"> 740 <conditional name="data_format">
817 <param name="data_format_select" value="bigwig" /> 741 <param name="data_format_select" value="bigwig"/>
818 <conditional name="useuri"> 742 <conditional name="useuri">
819 <param name="annotation" value="bw/merlin.bw" /> 743 <param name="annotation" value="bw/merlin.bw"/>
820 <param name="insource" value="history" /> 744 <param name="insource" value="history"/>
821 </conditional> 745 </conditional>
822 </conditional> 746 </conditional>
823 </repeat> 747 </repeat>
824 </repeat> 748 </repeat>
825 </repeat> 749 </repeat>
826 <param name="uglyTestingHack" value="enabled" /> 750 <param name="uglyTestingHack" value="enabled"/>
827 <output name="output"> 751 <output name="output">
828 <assert_contents> 752 <assert_contents>
829 <has_text text="genome path="></has_text> 753 <has_text text="genome path="/>
830 <has_text text="label="></has_text> 754 <has_text text="label="/>
831 <has_text text="format="></has_text> 755 <has_text text="format="/>
832 <has_text text="metadata"></has_text> 756 <has_text text="metadata"/>
833 <has_text text="useuri="></has_text> 757 <has_text text="useuri="/>
834 <has_text text="trackFile path="></has_text> 758 <has_text text="trackFile path="/>
835 <has_text text="ext=&quot;bigwig&quot;"></has_text> 759 <has_text text="ext=&quot;bigwig&quot;"/>
836 <has_text text="format=&quot;bigwig&quot;"></has_text> 760 <has_text text="format=&quot;bigwig&quot;"/>
837 </assert_contents> 761 </assert_contents>
838 </output> 762 </output>
839 </test> 763 </test>
840 <test> 764 <test>
841 <repeat name="assemblies"> 765 <repeat name="assemblies">
842 <conditional name="reference_genome"> 766 <conditional name="reference_genome">
843 <param name="genome_type_select" value="history" /> 767 <param name="genome_type_select" value="history"/>
844 <param name="genome" value="merlin.fa" /> 768 <param name="genome" value="merlin.fa"/>
845 <param name="genome.ext" value="fasta" /> 769 <param name="genome.ext" value="fasta"/>
846 <param name="genome.name" value="Merlin" /> 770 <param name="genome.name" value="Merlin"/>
847 </conditional> 771 </conditional>
848 <repeat name="track_groups"> 772 <repeat name="track_groups">
849 <param name="category" value="Default" /> 773 <param name="category" value="Default"/>
850 <repeat name="data_tracks"> 774 <repeat name="data_tracks">
851 <conditional name="data_format"> 775 <conditional name="data_format">
852 <param name="data_format_select" value="vcf" /> 776 <param name="data_format_select" value="vcf"/>
853 <conditional name="useuri"> 777 <conditional name="useuri">
854 <param name="insource" value="history" /> 778 <param name="insource" value="history"/>
855 <param name="annotation" value="vcf/merlin.vcf" /> 779 <param name="annotation" value="vcf/merlin.vcf"/>
856 </conditional> 780 </conditional>
857 </conditional> 781 </conditional>
858 </repeat> 782 </repeat>
859 </repeat> 783 </repeat>
860 </repeat> 784 </repeat>
861 <param name="uglyTestingHack" value="enabled" /> 785 <param name="uglyTestingHack" value="enabled"/>
862 <output name="output"> 786 <output name="output">
863 <assert_contents> 787 <assert_contents>
864 <has_text text="genome path="></has_text> 788 <has_text text="genome path="/>
865 <has_text text="label="></has_text> 789 <has_text text="label="/>
866 <has_text text="format="></has_text> 790 <has_text text="format="/>
867 <has_text text="metadata"></has_text> 791 <has_text text="metadata"/>
868 <has_text text="useuri="></has_text> 792 <has_text text="useuri="/>
869 <has_text text="trackFile path="></has_text> 793 <has_text text="trackFile path="/>
870 <has_text text="ext=&quot;vcf&quot; label=&quot;merlin.vcf&quot;"></has_text> 794 <has_text text="ext=&quot;vcf&quot; label=&quot;merlin.vcf&quot;"/>
871 </assert_contents> 795 </assert_contents>
872 </output> 796 </output>
873 </test> 797 </test>
874 <test> 798 <test>
875 <repeat name="assemblies"> 799 <repeat name="assemblies">
876 <conditional name="reference_genome"> 800 <conditional name="reference_genome">
877 <param name="genome_type_select" value="history" /> 801 <param name="genome_type_select" value="history"/>
878 <param name="genome" value="merlin.fa" /> 802 <param name="genome" value="merlin.fa"/>
879 <param name="genome.ext" value="fasta" /> 803 <param name="genome.ext" value="fasta"/>
880 <param name="genome.name" value="Merlin" /> 804 <param name="genome.name" value="Merlin"/>
881 </conditional> 805 </conditional>
882 </repeat> 806 </repeat>
883 <param name="uglyTestingHack" value="enabled" /> 807 <param name="uglyTestingHack" value="enabled"/>
884 <output name="output"> 808 <output name="output">
885 <assert_contents> 809 <assert_contents>
886 <has_text text="genome path="></has_text> 810 <has_text text="genome path="/>
887 <has_text text="label="></has_text> 811 <has_text text="label="/>
888 <has_text text="useuri="></has_text> 812 <has_text text="useuri="/>
889 <has_text text="metadata"></has_text> 813 <has_text text="metadata"/>
890 </assert_contents> 814 </assert_contents>
891 </output> 815 </output>
892 </test> 816 </test>
893 <test> 817 <test>
894 <repeat name="assemblies"> 818 <repeat name="assemblies">
895 <conditional name="reference_genome"> 819 <conditional name="reference_genome">
896 <param name="genome_type_select" value="history" /> 820 <param name="genome_type_select" value="history"/>
897 <param name="genome" value="merlin.fa" /> 821 <param name="genome" value="merlin.fa"/>
898 <param name="genome.ext" value="fasta" /> 822 <param name="genome.ext" value="fasta"/>
899 <param name="genome.name" value="Merlin" /> 823 <param name="genome.name" value="Merlin"/>
900 </conditional> 824 </conditional>
901 <repeat name="track_groups"> 825 <repeat name="track_groups">
902 <param name="category" value="Default" /> 826 <param name="category" value="Default"/>
903 <repeat name="data_tracks"> 827 <repeat name="data_tracks">
904 <conditional name="data_format"> 828 <conditional name="data_format">
905 <param name="data_format_select" value="vcf" /> 829 <param name="data_format_select" value="vcf"/>
906 <conditional name="useuri"> 830 <conditional name="useuri">
907 <param name="insource" value="history" /> 831 <param name="insource" value="history"/>
908 <param name="annotation" value="vcf/merlin.vcf" /> 832 <param name="annotation" value="vcf/merlin.vcf"/>
909 </conditional> 833 </conditional>
910 </conditional> 834 </conditional>
911 </repeat> 835 </repeat>
912 </repeat> 836 </repeat>
913 </repeat> 837 </repeat>
914 <param name="uglyTestingHack" value="enabled" /> 838 <param name="uglyTestingHack" value="enabled"/>
915 <output name="output"> 839 <output name="output">
916 <assert_contents> 840 <assert_contents>
917 <has_text text="genome path="></has_text> 841 <has_text text="genome path="/>
918 <has_text text="label="></has_text> 842 <has_text text="label="/>
919 <has_text text="format="></has_text> 843 <has_text text="format="/>
920 <has_text text="metadata"></has_text> 844 <has_text text="metadata"/>
921 <has_text text="useuri="></has_text> 845 <has_text text="useuri="/>
922 <has_text text="trackFile path="></has_text> 846 <has_text text="trackFile path="/>
923 <has_text text="ext=&quot;vcf&quot; label=&quot;merlin.vcf&quot;"></has_text> 847 <has_text text="ext=&quot;vcf&quot; label=&quot;merlin.vcf&quot;"/>
924 </assert_contents> 848 </assert_contents>
925 </output> 849 </output>
926 </test> 850 </test>
927 <test> 851 <test>
928 <repeat name="assemblies"> 852 <repeat name="assemblies">
929 <conditional name="reference_genome"> 853 <conditional name="reference_genome">
930 <param name="genome_type_select" value="history" /> 854 <param name="genome_type_select" value="history"/>
931 <param name="genome" value="merlin.fa" /> 855 <param name="genome" value="merlin.fa"/>
932 <param name="genome.ext" value="fasta" /> 856 <param name="genome.ext" value="fasta"/>
933 <param name="genome.name" value="Merlin" /> 857 <param name="genome.name" value="Merlin"/>
934 </conditional> 858 </conditional>
935 <repeat name="track_groups"> 859 <repeat name="track_groups">
936 <param name="category" value="Default" /> 860 <param name="category" value="Default"/>
937 <repeat name="data_tracks"> 861 <repeat name="data_tracks">
938 <conditional name="data_format"> 862 <conditional name="data_format">
939 <param name="data_format_select" value="gff" /> 863 <param name="data_format_select" value="gff"/>
940 <conditional name="useuri"> 864 <conditional name="useuri">
941 <param name="insource" value="history" /> 865 <param name="insource" value="history"/>
942 <param name="annotation" value="gff3/A.gff" /> 866 <param name="annotation" value="gff3/A.gff"/>
943 </conditional> 867 </conditional>
944 </conditional> 868 </conditional>
945 <conditional name="match_part"> 869 <conditional name="match_part">
946 <param name="match_part_select" value="false" /> 870 <param name="match_part_select" value="false"/>
947 </conditional> 871 </conditional>
948 <section name="jbcolor_scale"> 872 <section name="jbcolor_scale">
949 <conditional name="color_score"> 873 <conditional name="color_score">
950 <param name="color_score_select" value="none" /> 874 <param name="color_score_select" value="none"/>
951 </conditional> 875 </conditional>
952 <conditional name="color"> 876 <conditional name="color">
953 <param name="color_select" value="automatic" /> 877 <param name="color_select" value="automatic"/>
954 </conditional> 878 </conditional>
955 </section> 879 </section>
956 </repeat> 880 </repeat>
957 </repeat> 881 </repeat>
958 <repeat name="track_groups"> 882 <repeat name="track_groups">
959 <param name="category" value="Ignore Scale" /> 883 <param name="category" value="Ignore Scale"/>
960 <repeat name="data_tracks"> 884 <repeat name="data_tracks">
961 <conditional name="data_format"> 885 <conditional name="data_format">
962 <param name="data_format_select" value="gff" /> 886 <param name="data_format_select" value="gff"/>
963 <conditional name="useuri"> 887 <conditional name="useuri">
964 <param name="insource" value="history" /> 888 <param name="insource" value="history"/>
965 <param name="annotation" value="gff3/1.gff" /> 889 <param name="annotation" value="gff3/1.gff"/>
966 </conditional> 890 </conditional>
967 <conditional name="match_part"> 891 <conditional name="match_part">
968 <param name="match_part_select" value="false" /> 892 <param name="match_part_select" value="false"/>
969 </conditional> 893 </conditional>
970 <section name="jbcolor_scale"> 894 <section name="jbcolor_scale">
971 <conditional name="color_score"> 895 <conditional name="color_score">
972 <param name="color_score_select" value="none" /> 896 <param name="color_score_select" value="none"/>
973 <conditional name="color"> 897 <conditional name="color">
974 <param name="color_select" value="manual" /> 898 <param name="color_select" value="manual"/>
975 <param name="style_color" value="#ff00ff" /> 899 <param name="style_color" value="#ff00ff"/>
976 </conditional> 900 </conditional>
977 </conditional> 901 </conditional>
978 </section> 902 </section>
979 </conditional> 903 </conditional>
980 </repeat> 904 </repeat>
981 </repeat> 905 </repeat>
982 <repeat name="track_groups"> 906 <repeat name="track_groups">
983 <param name="category" value="Scaled Colour" /> 907 <param name="category" value="Scaled Colour"/>
984 <repeat name="data_tracks"> 908 <repeat name="data_tracks">
985 <conditional name="data_format"> 909 <conditional name="data_format">
986 <param name="data_format_select" value="gff" /> 910 <param name="data_format_select" value="gff"/>
987 <conditional name="useuri"> 911 <conditional name="useuri">
988 <param name="insource" value="history" /> 912 <param name="insource" value="history"/>
989 <param name="annotation" value="gff3/C.gff" /> 913 <param name="annotation" value="gff3/C.gff"/>
990 </conditional> 914 </conditional>
991 <conditional name="match_part"> 915 <conditional name="match_part">
992 <param name="match_part_select" value="false" /> 916 <param name="match_part_select" value="false"/>
993 </conditional> 917 </conditional>
994 <section name="jbcolor_scale"> 918 <section name="jbcolor_scale">
995 <conditional name="color_score"> 919 <conditional name="color_score">
996 <param name="color_score_select" value="score" /> 920 <param name="color_score_select" value="score"/>
997 <param name="score_scaling" value="linear" /> 921 <param name="score_scaling" value="linear"/>
998 <conditional name="score_scales"> 922 <conditional name="score_scales">
999 <param name="scale_select" value="automatic" /> 923 <param name="scale_select" value="automatic"/>
1000 </conditional> 924 </conditional>
1001 <conditional name="color_scheme"> 925 <conditional name="color_scheme">
1002 <param name="score_scheme" value="opacity" /> 926 <param name="score_scheme" value="opacity"/>
1003 <conditional name="color"> 927 <conditional name="color">
1004 <param name="color_select" value="automatic" /> 928 <param name="color_select" value="automatic"/>
1005 </conditional> 929 </conditional>
1006 </conditional> 930 </conditional>
1007 </conditional> 931 </conditional>
1008 </section> 932 </section>
1009 </conditional> 933 </conditional>
1010 </repeat> 934 </repeat>
1011 <repeat name="data_tracks"> 935 <repeat name="data_tracks">
1012 <conditional name="data_format"> 936 <conditional name="data_format">
1013 <param name="data_format_select" value="gff" /> 937 <param name="data_format_select" value="gff"/>
1014 <conditional name="useuri"> 938 <conditional name="useuri">
1015 <param name="annotation" value="gff3/B.gff" /> 939 <param name="annotation" value="gff3/B.gff"/>
1016 <param name="insource" value="history" /> 940 <param name="insource" value="history"/>
1017 </conditional> 941 </conditional>
1018 <conditional name="match_part"> 942 <conditional name="match_part">
1019 <param name="match_part_select" value="false" /> 943 <param name="match_part_select" value="false"/>
1020 </conditional> 944 </conditional>
1021 <section name="jbcolor_scale"> 945 <section name="jbcolor_scale">
1022 <conditional name="color_score"> 946 <conditional name="color_score">
1023 <param name="color_score_select" value="score" /> 947 <param name="color_score_select" value="score"/>
1024 <param name="score_scaling" value="linear" /> 948 <param name="score_scaling" value="linear"/>
1025 <conditional name="score_scales"> 949 <conditional name="score_scales">
1026 <param name="scale_select" value="automatic" /> 950 <param name="scale_select" value="automatic"/>
1027 </conditional> 951 </conditional>
1028 <conditional name="color_scheme"> 952 <conditional name="color_scheme">
1029 <param name="score_scheme" value="opacity" /> 953 <param name="score_scheme" value="opacity"/>
1030 <conditional name="color"> 954 <conditional name="color">
1031 <param name="color_select" value="manual" /> 955 <param name="color_select" value="manual"/>
1032 <param name="style_color" value="#0000ff" /> 956 <param name="style_color" value="#0000ff"/>
1033 </conditional> 957 </conditional>
1034 </conditional> 958 </conditional>
1035 </conditional> 959 </conditional>
1036 </section> 960 </section>
1037 </conditional> 961 </conditional>
1038 </repeat> 962 </repeat>
1039 <repeat name="data_tracks"> 963 <repeat name="data_tracks">
1040 <conditional name="data_format"> 964 <conditional name="data_format">
1041 <param name="data_format_select" value="gff" /> 965 <param name="data_format_select" value="gff"/>
1042 <conditional name="useuri"> 966 <conditional name="useuri">
1043 <param name="annotation" value="gff3/A.gff" /> 967 <param name="annotation" value="gff3/A.gff"/>
1044 <param name="insource" value="history" /> 968 <param name="insource" value="history"/>
1045 </conditional> 969 </conditional>
1046 <conditional name="match_part"> 970 <conditional name="match_part">
1047 <param name="match_part_select" value="false" /> 971 <param name="match_part_select" value="false"/>
1048 </conditional> 972 </conditional>
1049 <section name="jbcolor_scale"> 973 <section name="jbcolor_scale">
1050 <conditional name="color_score"> 974 <conditional name="color_score">
1051 <param name="color_score_select" value="score" /> 975 <param name="color_score_select" value="score"/>
1052 <param name="score_scaling" value="linear" /> 976 <param name="score_scaling" value="linear"/>
1053 <conditional name="score_scales"> 977 <conditional name="score_scales">
1054 <param name="scale_select" value="manual" /> 978 <param name="scale_select" value="manual"/>
1055 <param name="minimum" value="0" /> 979 <param name="minimum" value="0"/>
1056 <param name="maximum" value="1000" /> 980 <param name="maximum" value="1000"/>
1057 </conditional> 981 </conditional>
1058 <conditional name="color_scheme"> 982 <conditional name="color_scheme">
1059 <param name="score_scheme" value="opacity" /> 983 <param name="score_scheme" value="opacity"/>
1060 <conditional name="color"> 984 <conditional name="color">
1061 <param name="color_select" value="automatic" /> 985 <param name="color_select" value="automatic"/>
1062 </conditional> 986 </conditional>
1063 </conditional> 987 </conditional>
1064 </conditional> 988 </conditional>
1065 </section> 989 </section>
1066 </conditional> 990 </conditional>
1067 </repeat> 991 </repeat>
1068 <repeat name="data_tracks"> 992 <repeat name="data_tracks">
1069 <conditional name="data_format"> 993 <conditional name="data_format">
1070 <param name="data_format_select" value="gff" /> 994 <param name="data_format_select" value="gff"/>
1071 <conditional name="useuri"> 995 <conditional name="useuri">
1072 <param name="annotation" value="gff3/1.gff" /> 996 <param name="annotation" value="gff3/1.gff"/>
1073 <param name="insource" value="history" /> 997 <param name="insource" value="history"/>
1074 </conditional> 998 </conditional>
1075 <conditional name="match_part"> 999 <conditional name="match_part">
1076 <param name="match_part_select" value="false" /> 1000 <param name="match_part_select" value="false"/>
1077 </conditional> 1001 </conditional>
1078 <section name="jbcolor_scale"> 1002 <section name="jbcolor_scale">
1079 <conditional name="color_score"> 1003 <conditional name="color_score">
1080 <param name="color_score_select" value="score" /> 1004 <param name="color_score_select" value="score"/>
1081 <param name="score_scaling" value="linear" /> 1005 <param name="score_scaling" value="linear"/>
1082 <conditional name="score_scales"> 1006 <conditional name="score_scales">
1083 <param name="scale_select" value="manual" /> 1007 <param name="scale_select" value="manual"/>
1084 <param name="minimum" value="0" /> 1008 <param name="minimum" value="0"/>
1085 <param name="maximum" value="1000" /> 1009 <param name="maximum" value="1000"/>
1086 </conditional> 1010 </conditional>
1087 <conditional name="color_scheme"> 1011 <conditional name="color_scheme">
1088 <param name="score_scheme" value="opacity" /> 1012 <param name="score_scheme" value="opacity"/>
1089 <conditional name="color"> 1013 <conditional name="color">
1090 <param name="color_select" value="manual" /> 1014 <param name="color_select" value="manual"/>
1091 <param name="style_color" value="#ff0000" /> 1015 <param name="style_color" value="#ff0000"/>
1092 </conditional> 1016 </conditional>
1093 </conditional> 1017 </conditional>
1094 </conditional> 1018 </conditional>
1095 </section> 1019 </section>
1096 </conditional> 1020 </conditional>
1097 </repeat> 1021 </repeat>
1098 </repeat> 1022 </repeat>
1099 <repeat name="track_groups"> 1023 <repeat name="track_groups">
1100 <param name="category" value="Realistic" /> 1024 <param name="category" value="Realistic"/>
1101 <repeat name="data_tracks"> 1025 <repeat name="data_tracks">
1102 <conditional name="data_format"> 1026 <conditional name="data_format">
1103 <param name="data_format_select" value="gff" /> 1027 <param name="data_format_select" value="gff"/>
1104 <conditional name="useuri"> 1028 <conditional name="useuri">
1105 <param name="annotation" value="gff3/interpro.gff" /> 1029 <param name="annotation" value="gff3/interpro.gff"/>
1106 <param name="insource" value="history" /> 1030 <param name="insource" value="history"/>
1107 </conditional> 1031 </conditional>
1108 <conditional name="match_part"> 1032 <conditional name="match_part">
1109 <param name="match_part_select" value="false" /> 1033 <param name="match_part_select" value="false"/>
1110 </conditional> 1034 </conditional>
1111 <section name="jbcolor_scale"> 1035 <section name="jbcolor_scale">
1112 <conditional name="color_score"> 1036 <conditional name="color_score">
1113 <param name="color_score_select" value="none" /> 1037 <param name="color_score_select" value="none"/>
1114 </conditional> 1038 </conditional>
1115 <conditional name="color"> 1039 <conditional name="color">
1116 <param name="color_select" value="automatic" /> 1040 <param name="color_select" value="automatic"/>
1117 </conditional> 1041 </conditional>
1118 </section> 1042 </section>
1119 </conditional> 1043 </conditional>
1120 </repeat> 1044 </repeat>
1121 <repeat name="data_tracks"> 1045 <repeat name="data_tracks">
1122 <conditional name="data_format"> 1046 <conditional name="data_format">
1123 <param name="data_format_select" value="gff" /> 1047 <param name="data_format_select" value="gff"/>
1124 <conditional name="useuri"> 1048 <conditional name="useuri">
1125 <param name="annotation" value="gff3/2.gff" /> 1049 <param name="annotation" value="gff3/2.gff"/>
1126 <param name="insource" value="history" /> 1050 <param name="insource" value="history"/>
1127 </conditional> 1051 </conditional>
1128 <conditional name="match_part"> 1052 <conditional name="match_part">
1129 <param name="match_part_select" value="true" /> 1053 <param name="match_part_select" value="true"/>
1130 <param name="name" value="cDNA_match" /> 1054 <param name="name" value="cDNA_match"/>
1131 </conditional> 1055 </conditional>
1132 <section name="jbcolor_scale"> 1056 <section name="jbcolor_scale">
1133 <conditional name="color_score"> 1057 <conditional name="color_score">
1134 <param name="color_score_select" value="none" /> 1058 <param name="color_score_select" value="none"/>
1135 </conditional> 1059 </conditional>
1136 <conditional name="color"> 1060 <conditional name="color">
1137 <param name="color_select" value="automatic" /> 1061 <param name="color_select" value="automatic"/>
1138 </conditional> 1062 </conditional>
1139 </section> 1063 </section>
1140 </conditional> 1064 </conditional>
1141 </repeat> 1065 </repeat>
1142 </repeat> 1066 </repeat>
1143 </repeat> 1067 </repeat>
1144 1068 <param name="uglyTestingHack" value="enabled"/>
1145 <param name="uglyTestingHack" value="enabled" />
1146 <output name="output"> 1069 <output name="output">
1147 <assert_contents> 1070 <assert_contents>
1148 <has_text text="Ignore Scale" /> 1071 <has_text text="Ignore Scale"/>
1149 <has_text text="A.gff" /> 1072 <has_text text="A.gff"/>
1150 <has_text text="B.gff" /> 1073 <has_text text="B.gff"/>
1151 <has_text text="C.gff" /> 1074 <has_text text="C.gff"/>
1152 <has_text text="interpro.gff" /> 1075 <has_text text="interpro.gff"/>
1153 <has_text text="Scaled Colour" /> 1076 <has_text text="Scaled Colour"/>
1154 <has_text text="1.gff" /> 1077 <has_text text="1.gff"/>
1155 <has_text text="2.gff" /> 1078 <has_text text="2.gff"/>
1156 </assert_contents> 1079 </assert_contents>
1157 </output> 1080 </output>
1158 </test> 1081 </test>
1159
1160 <!-- TODO add a synteny test --> 1082 <!-- TODO add a synteny test -->
1161 <!-- TODO add a bam and a cram test --> 1083 <!-- TODO add a bam and a cram test -->
1162 <!-- TODO add an hic test --> 1084 <!-- TODO add an hic test -->
1163 <!-- TODO add a vcf_bgzip test --> 1085 <!-- TODO add a vcf_bgzip test -->
1164 </tests> 1086 </tests>
1273 1195
1274 **Protein blast search** option merely informs underlying tools that 1196 **Protein blast search** option merely informs underlying tools that
1275 they should adjust feature locations by 3x. 1197 they should adjust feature locations by 3x.
1276 1198
1277 1199
1278 @ATTRIBUTION@
1279 ]]></help> 1200 ]]></help>
1280 <expand macro="citations" /> 1201 <expand macro="citations"/>
1202 <expand macro="creators"/>
1281 </tool> 1203 </tool>