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comparison hubArchiveCreator.xml @ 20:40469b265ddb draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
author yating-l
date Fri, 20 Jan 2017 17:12:03 -0500
parents d786bca6a75d
children 884ee2a71680
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19:0152500d9acd 20:40469b265ddb
3 This Galaxy tool permits to prepare your files to be ready for 3 This Galaxy tool permits to prepare your files to be ready for
4 Assembly Hub visualization. 4 Assembly Hub visualization.
5 </description> 5 </description>
6 6
7 <requirements> 7 <requirements>
8 <!-- Conda dependencies --> 8 <requirement type="package" version="1.0">ucsc_tools_340</requirement>
9 <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
10 <requirement type="package" version="332">ucsc-fatotwobit</requirement>
11 <requirement type="package" version="332">ucsc-genepredtobed</requirement>
12 <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement>
13 <requirement type="package" version="332">ucsc-gff3togenepred</requirement>
14 <requirement type="package" version="332">ucsc-gtftogenepred</requirement>
15 <!-- TODO: Change the conda ucsc-psltobigpsl and take one > v337 because of bugs before -->
16 <!-- <requirement type="package" version="332">ucsc-psltobigpsl</requirement> -->
17 <requirement type="package" version="332">ucsc-twobitinfo</requirement>
18 <requirement type="package" version="1.3">samtools</requirement>
19 <!-- ToolShed dependencies -->
20 <requirement type="package" version="312">ucsc_tools</requirement>
21 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement>
22 <requirement type="package" version="0.0.1">gtfToGenePred</requirement>
23 <requirement type="package" version="0.0.1">genePredToBed</requirement>
24 <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement>
25 <requirement type="package" version="0.0.1">pslToBigPsl</requirement>
26 <requirement type="package" version="1.2">samtools</requirement> 9 <requirement type="package" version="1.2">samtools</requirement>
27 </requirements> 10 </requirements>
28 11
29 <stdio> 12 <stdio>
30 <regex match="^pass1" 13 <regex match="^pass1"
36 </stdio> 19 </stdio>
37 20
38 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] --> 21 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
39 <command detect_errors="exit_code"><![CDATA[ 22 <command detect_errors="exit_code"><![CDATA[
40 mkdir -p $output.extra_files_path; 23 mkdir -p $output.extra_files_path;
24
41 python $__tool_directory__/hubArchiveCreator.py 25 python $__tool_directory__/hubArchiveCreator.py
42 26
43 ## Ask the user to enter the genome name 27 ## Ask the user to enter the genome name
44 --genome_name '$genome_name' 28 --genome_name '$genome_name'
45 29
98 #silent extra_data_dict.update({"index": $bam_index}) 82 #silent extra_data_dict.update({"index": $bam_index})
99 83
100 #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict) 84 #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict)
101 #end if 85 #end if
102 #if $f.formatChoice.format_select == "bed" 86 #if $f.formatChoice.format_select == "bed"
103 #if $f.formatChoice.bedChoice.bed_select == "bed" 87 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
104 --bed $f.formatChoice.bedChoice.BED 88 --bed $f.formatChoice.bedChoice.BED
105 #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final, 89 #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final,
106 extra_data_dict) 90 extra_data_dict)
107 #end if 91 #end if
108 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" 92 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
109 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats 93 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
110 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final, 94 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
95 extra_data_dict)
96 #end if
97 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
98 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
99 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
100 extra_data_dict)
101 #end if
102 #if $f.formatChoice.bedChoice.bed_select == "bigpsl_option"
103 --bigpsl $f.formatChoice.bedChoice.bigPsl
104 #silent $prepare_json($f.formatChoice.bedChoice.bigPsl, $index_track_final,
111 extra_data_dict) 105 extra_data_dict)
112 #end if 106 #end if
113 #end if 107 #end if
114 #if $f.formatChoice.format_select == "psl" 108 #if $f.formatChoice.format_select == "psl"
115 --psl $f.formatChoice.PSL 109 --psl $f.formatChoice.PSL
147 ## Retrieve the user email 141 ## Retrieve the user email
148 --user_email $__user_email__ 142 --user_email $__user_email__
149 143
150 -d $__tool_directory__ 144 -d $__tool_directory__
151 145
152 -e $output.files_path 146 -e $output.extra_files_path
153 147
154 $advanced_options.debug_mode 148 $advanced_options.debug_mode
155 149
156 -o $output; 150 -o $output;
151
157 ]]></command> 152 ]]></command>
158 153
159 <inputs> 154 <inputs>
160 <param 155 <param
161 name="genome_name" 156 name="genome_name"
200 </param> 195 </param>
201 </when> 196 </when>
202 <when value="bed"> 197 <when value="bed">
203 <conditional name="bedChoice"> 198 <conditional name="bedChoice">
204 <param name="bed_select" type="select" label="Bed Choice"> 199 <param name="bed_select" type="select" label="Bed Choice">
205 <option value="bed" selected="true">BED Generic (bed3+)</option> 200 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
206 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> 201 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
202 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
203 <option value="bigpsl_option">bigPsl (bed12+12 / bigPsl.as)</option>
207 </param> 204 </param>
208 <when value="bed"> 205 <when value="bed_generic">
209 <param 206 <param
210 format="bed" 207 format="bed"
211 name="BED" 208 name="BED"
212 type="data" 209 type="data"
213 label="Generic Bed File Choice" 210 label="Generic Bed File Choice"
218 <param 215 <param
219 format="bed" 216 format="bed"
220 name="BED_simple_repeats" 217 name="BED_simple_repeats"
221 type="data" 218 type="data"
222 label="Bed Simple Repeats (Bed4+12) File" 219 label="Bed Simple Repeats (Bed4+12) File"
220 />
221 </when>
222 <when value="bed_splice_junctions_option">
223 <param
224 format="bed"
225 name="BED_splice_junctions"
226 type="data"
227 label="Bed Splice Junctions (Bed12+1) File"
228 />
229 </when>
230 <when value="bigpsl_option">
231 <param
232 format="bed"
233 name="bigPsl"
234 type="data"
235 label="bigPsl (Bed12+12) File"
223 /> 236 />
224 </when> 237 </when>
225 </conditional> 238 </conditional>
226 <param name="track_color" type="color" label="Track color" value="#000000"> 239 <param name="track_color" type="color" label="Track color" value="#000000">
227 <sanitizer> 240 <sanitizer>
320 <outputs> 333 <outputs>
321 <data format="trackhub" name="output"/> 334 <data format="trackhub" name="output"/>
322 </outputs> 335 </outputs>
323 336
324 <tests> 337 <tests>
325 <!-- Can also use assert_command to test command --> 338 <!-- Test with only the fasta file -->
326 <!-- Testing GFF3 input --> 339 <test>
327 <test> 340 <param name="genome_name" value="Dbia3"/>
328 <param name="fasta_file" value="dbia3.fa"/> 341 <param name="fasta_file" value="common/dbia3.fa"/>
329 <repeat name="format"> 342 <output name="output" file="only_genome/only_genome.html">
330 <conditional name="formatChoice"> 343 <extra_files type="file" name="__main__.log" value="only_genome/__main__.log" />
331 <param name="format_select" value="gff3"/> 344 <extra_files type="file" name="myHub/genomes.txt" value="only_genome/myHub/genomes.txt" />
332 <param name="GFF3" value="augustusDbia3.gff3"/> 345 <extra_files type="file" name="myHub/Dbia3.html" value="only_genome/myHub/Dbia3.html"/>
333 </conditional> 346 <!-- Email could be different, but we need to ensure we still have the email line -->
334 </repeat> 347 <extra_files type="file" name="myHub/hub.txt" value="only_genome/myHub/hub.txt" lines_diff="2">
335 <repeat name="format"> 348 <assert_contents>
336 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> 349 <has_text text="email"/>
337 <!-- TODO: Ask why the tests are not passing with this xml: 350 </assert_contents>
338 Error creating a job for these tool inputs - Error executing tool: 'NoneType' object has no attribute 'current_history' 351 </extra_files>
339 <conditional name="formatChoice"> 352 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
340 <param name="format_select" value="bed"/> 353 </extra_files>
341 <conditional name="bedChoice"> 354 <extra_files type="file" name="myHub/Dbia3/description.html" value="only_genome/myHub/Dbia3/description.html"/>
342 <param name="bed_select" value="bed_simple_repeats_option"/> 355 </output>
343 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> 356 </test>
344 </conditional> 357
345 </conditional> 358 <!-- Test with Bam -->
346 --> 359 <test>
347 </repeat> 360 <param name="genome_name" value="Dbia3"/>
348 361 <param name="fasta_file" value="common/dbia3.fa"/>
349 <output name="output"> 362 <repeat name="group">
350 <assert_contents> 363 <param name="group_name" value="Default group"/>
351 <has_text text="myHub"/> 364 <repeat name="format">
352 </assert_contents> 365 <conditional name="formatChoice">
353 <assert_contents> 366 <param name="format_select" value="bam"/>
354 <has_text text="dbia3_trfBig.bb"/> 367 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
355 </assert_contents> 368 <param name="track_color" value="#000000"/>
356 <assert_contents> 369 </conditional>
357 <has_text text="SAODOAii qwwqod92921"/> 370 </repeat>
358 </assert_contents> 371 </repeat>
359 </output> 372 <output name="output" file="bam/bam.html">
360 </test> 373 <!-- Verify tracks folder contains bam and bai -->
361 <test> 374 <extra_files type="file"
362 <param name="fasta_file" value="dbia3.fa"/> 375 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
363 <param name="GFF3" value="augustusDbia3.gff3"/> 376 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
364 <output name="output" file="augustusOutput.html" lines_diff="2"> 377 compare="sim_size"
365 <extra_files type="directory" value="myHub"/> 378 />
366 <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/> 379 <extra_files type="file"
367 </output> 380 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
368 </test> 381 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
369 <!-- Testing Generic BED input --> 382 compare="sim_size"
370 <!-- Testing Bed Simple repeat input --> 383 />
384 <!-- Verify trackDb.txt contains the basic fields for a bam -->
385 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="bam/myHub/Dbia3/trackDb.txt">
386 <assert_contents>
387 <has_text text="track"/>
388 <has_text text="longLabel"/>
389 <has_text text="shortLabel"/>
390 <has_text text="bigDataUrl"/>
391 <has_text text="type"/>
392 <has_text text="visibility"/>
393 <has_text text="thickDrawItem"/>
394 <has_text text="priority"/>
395 <has_text text="color"/>
396 <has_text text="group"/>
397 </assert_contents>
398 </extra_files>
399 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
400 </output>
401 </test>
402
403 <!-- Test with Bed Generic -->
404 <test>
405 <param name="genome_name" value="Dbia3"/>
406 <param name="fasta_file" value="common/dbia3.fa"/>
407 <repeat name="group">
408 <param name="group_name" value="Default group"/>
409 <repeat name="format">
410 <conditional name="formatChoice">
411 <param name="format_select" value="bed" />
412 <conditional name="bedChoice">
413 <param name="bed_select" value="bed_generic"/>
414 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
415 <param name="track_color" value="#000000"/>
416 </conditional>
417 </conditional>
418 </repeat>
419 </repeat>
420 <output name="output" file="bed_generic/bed_generic.html">
421 <!-- Verify tracks folder contains bam and bai -->
422 <extra_files type="file"
423 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
424 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
425 compare="sim_size"
426 />
427 </output>
428 </test>
429
430 <!-- Test with Bed Simple repeat -->
431 <test>
432 <param name="genome_name" value="Dbia3"/>
433 <param name="fasta_file" value="common/dbia3.fa"/>
434 <repeat name="group">
435 <param name="group_name" value="Default group"/>
436 <repeat name="format">
437 <conditional name="formatChoice">
438 <param name="format_select" value="bed" />
439 <conditional name="bedChoice">
440 <param name="bed_select" value="bed_simple_repeats_option"/>
441 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
442 <param name="track_color" value="#000000"/>
443 </conditional>
444 </conditional>
445 </repeat>
446 </repeat>
447 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
448 <!-- Verify tracks folder contains bam and bai -->
449 <extra_files type="file"
450 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
451 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
452 compare="sim_size"
453 />
454 </output>
455 </test>
456
457
458 <!-- Test with Psl -->
459 <test>
460 <param name="genome_name" value="Dbia3"/>
461 <param name="fasta_file" value="common/dbia3.fa"/>
462 <repeat name="group">
463 <param name="group_name" value="Default group"/>
464 <repeat name="format">
465 <conditional name="formatChoice">
466 <param name="format_select" value="psl"/>
467 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
468 <param name="track_color" value="#000000"/>
469 </conditional>
470 </repeat>
471 </repeat>
472 <output name="output" file="psl/psl_trackhub.html">
473 <!-- Verify tracks folder contains bam and bai -->
474 <extra_files type="file"
475 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
476 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
477 compare="sim_size"
478 />
479 <!-- Verify trackDb.txt contains the basic fields for a bam -->
480 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
481 </output>
482 </test>
483
484 <!-- Test with BigWig -->
485 <test>
486 <param name="genome_name" value="Dbia3"/>
487 <param name="fasta_file" value="common/dbia3.fa"/>
488 <repeat name="group">
489 <param name="group_name" value="Default group"/>
490 <repeat name="format">
491 <conditional name="formatChoice">
492 <param name="format_select" value="bigwig"/>
493 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
494 <param name="track_color" value="#000000"/>
495 </conditional>
496 </repeat>
497 </repeat>
498 <output name="output" file="bigwig/bigwig.html">
499 <!-- Verify tracks folder contains bam and bai -->
500 <extra_files type="file"
501 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
502 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
503 compare="sim_size"
504 />
505 <!-- Verify trackDb.txt contains the basic fields for a bam -->
506 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
507 </output>
508 </test>
509
510 <!-- Test with GFF3 -->
511 <test>
512 <param name="genome_name" value="Dbia3"/>
513 <param name="fasta_file" value="common/dbia3.fa"/>
514 <repeat name="group">
515 <param name="group_name" value="Default group"/>
516 <repeat name="format">
517 <conditional name="formatChoice">
518 <param name="format_select" value="gff3"/>
519 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
520 <param name="track_color" value="#000000"/>
521 </conditional>
522 </repeat>
523 </repeat>
524 <output name="output" file="gff3/gff3_trackhub.html">
525 <!-- Verify tracks folder contains bam and bai -->
526 <extra_files type="file"
527 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
528 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
529 compare="sim_size"
530 />
531 <!-- Verify trackDb.txt contains the basic fields for a bam -->
532 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
533 </output>
534 </test>
535
536 <!-- Test with GTF -->
537 <test>
538 <param name="genome_name" value="Dbia3"/>
539 <param name="fasta_file" value="common/dbia3.fa"/>
540 <repeat name="group">
541 <param name="group_name" value="Default group"/>
542 <repeat name="format">
543 <conditional name="formatChoice">
544 <param name="format_select" value="gtf"/>
545 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
546 <param name="track_color" value="#000000"/>
547 </conditional>
548 </repeat>
549 </repeat>
550 <output name="output" file="gtf/gtf_trackhub.html">
551 <!-- Verify tracks folder contains bam and bai -->
552 <extra_files type="file"
553 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
554 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
555 compare="sim_size"
556 />
557 <!-- Verify trackDb.txt contains the basic fields for a bam -->
558 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
559 </output>
560 </test>
561
562 <!-- Test with one group and multiple tracks -->
563 <test>
564 <param name="genome_name" value="Dbia3"/>
565 <param name="fasta_file" value="common/dbia3.fa"/>
566 <repeat name="group">
567 <param name="group_name" value="Default group"/>
568 <repeat name="format">
569 <conditional name="formatChoice">
570 <param name="format_select" value="gtf"/>
571 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
572 <param name="track_color" value="#000000"/>
573 </conditional>
574 </repeat>
575 <repeat name="format">
576 <conditional name="formatChoice">
577 <param name="format_select" value="gff3"/>
578 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
579 <param name="track_color" value="#000000"/>
580 </conditional>
581 </repeat>
582 </repeat>
583 <output name="output" file="gtf_gff/gtf_gff_trackhub.html">
584 <!-- verify tracks folder contains bam and bai -->
585 <extra_files type="file"
586 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
587 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
588 compare="sim_size"
589 />
590 <extra_files type="file"
591 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
592 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
593 compare="sim_size"
594 />
595 <!-- verify trackdb.txt contains the basic fields for a bam -->
596 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
597 </output>
598 </test>
599
600 <!-- Test with one group and all the supported datatypes on 10/04/2016 -->
601 <test>
602 <param name="genome_name" value="Dbia3"/>
603 <param name="fasta_file" value="common/dbia3.fa"/>
604 <repeat name="group">
605 <param name="group_name" value="Default group"/>
606 <repeat name="format">
607 <conditional name="formatChoice">
608 <param name="format_select" value="bam"/>
609 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
610 <param name="track_color" value="#000000"/>
611 </conditional>
612 </repeat>
613 <repeat name="format">
614 <conditional name="formatChoice">
615 <param name="format_select" value="bed"/>
616 <conditional name="bedChoice">
617 <param name="bed_select" value="bed_generic"/>
618 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
619 <param name="track_color" value="#000000"/>
620 </conditional>
621 </conditional>
622 </repeat>
623 <repeat name="format">
624 <conditional name="formatChoice">
625 <param name="format_select" value="bed"/>
626 <conditional name="bedChoice">
627 <param name="bed_select" value="bed_simple_repeats_option"/>
628 <param name="BED_simple_repeats" ftype="bed"
629 value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
630 <param name="track_color" value="#000000"/>
631 </conditional>
632 </conditional>
633 </repeat>
634 <repeat name="format">
635 <conditional name="formatChoice">
636 <param name="format_select" value="psl"/>
637 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
638 <param name="track_color" value="#000000"/>
639 </conditional>
640 </repeat>
641 <repeat name="format">
642 <conditional name="formatChoice">
643 <param name="format_select" value="bigwig"/>
644 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
645 <param name="track_color" value="#000000"/>
646 </conditional>
647 </repeat>
648 <repeat name="format">
649 <conditional name="formatChoice">
650 <param name="format_select" value="gff3"/>
651 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
652 <param name="track_color" value="#000000"/>
653 </conditional>
654 </repeat>
655 <repeat name="format">
656 <conditional name="formatChoice">
657 <param name="format_select" value="gtf"/>
658 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
659 <param name="track_color" value="#000000"/>
660 </conditional>
661 </repeat>
662 </repeat>
663 <output name="output" file="all_datatypes/all_datatypes_trackhub.html">
664 <!-- verify tracks folder contains all the files -->
665 <extra_files type="file"
666 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
667 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
668 compare="sim_size"
669 />
670 <extra_files type="file"
671 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
672 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
673 compare="sim_size"
674 />
675 <extra_files type="file"
676 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
677 value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
678 compare="sim_size"
679 />
680 <extra_files type="file"
681 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
682 value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
683 compare="sim_size"
684 />
685 <extra_files type="file"
686 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
687 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb"
688 compare="sim_size"
689 />
690 <extra_files type="file"
691 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
692 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
693 compare="sim_size"
694 />
695 <extra_files type="file"
696 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
697 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
698 compare="sim_size"
699 />
700 <extra_files type="file"
701 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
702 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
703 compare="sim_size"
704 />
705 <!-- verify trackdb.txt contains the basic fields for a bam -->
706 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
707 </output>
708 </test>
709
710 <!-- Test with two groups and no tracks -->
711 <test>
712 <param name="genome_name" value="Dbia3"/>
713 <param name="fasta_file" value="common/dbia3.fa"/>
714 <repeat name="group">
715 <param name="group_name" value="Default group"/>
716 </repeat>
717 <repeat name="group">
718 <param name="group_name" value="Other group"/>
719 </repeat>
720 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
721 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_no_track/myHub/genomes.txt"/>
722 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_no_track/myHub/Dbia3.html"/>
723 <!-- Email could be different, but we need to ensure we still have the email line -->
724 <extra_files type="file" name="myHub/hub.txt" value="two_groups_no_track/myHub/hub.txt" lines_diff="2">
725 <assert_contents>
726 <has_text text="email"/>
727 </assert_contents>
728 </extra_files>
729 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
730 </extra_files>
731 <extra_files type="file" name="myHub/Dbia3/description.html"
732 value="two_groups_no_track/myHub/Dbia3/description.html"/>
733 </output>
734 </test>
735
736 <!-- Test with two groups and one track in first -->
737 <test>
738 <param name="genome_name" value="Dbia3"/>
739 <param name="fasta_file" value="common/dbia3.fa"/>
740 <repeat name="group">
741 <param name="group_name" value="Default group"/>
742 <repeat name="format">
743 <conditional name="formatChoice">
744 <param name="format_select" value="bigwig"/>
745 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
746 <param name="track_color" value="#000000"/>
747 </conditional>
748 </repeat>
749 </repeat>
750 <repeat name="group">
751 <param name="group_name" value="Other group"/>
752 </repeat>
753 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">
754 <!-- Check myHub structure -->
755 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_first/myHub/genomes.txt"/>
756 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_first/myHub/Dbia3.html"/>
757 <!-- Email could be different, but we need to ensure we still have the email line -->
758 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_first/myHub/hub.txt" lines_diff="2">
759 <assert_contents>
760 <has_text text="email"/>
761 </assert_contents>
762 </extra_files>
763 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
764 </extra_files>
765 <extra_files type="file" name="myHub/Dbia3/description.html"
766 value="two_groups_one_track_first/myHub/Dbia3/description.html"/>
767
768 <!-- Check tracks exist -->
769 <extra_files type="file"
770 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
771 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
772 compare="sim_size"
773 />
774
775 <!-- Check the groups.txt exists and is properly populated -->
776 </output>
777 </test>
778
779 <!-- Test with two groups and one track in both -->
780 <test>
781 <param name="genome_name" value="Dbia3"/>
782 <param name="fasta_file" value="common/dbia3.fa"/>
783 <repeat name="group">
784 <param name="group_name" value="Default group"/>
785 <repeat name="format">
786 <conditional name="formatChoice">
787 <param name="format_select" value="bigwig"/>
788 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
789 <param name="track_color" value="#000000"/>
790 </conditional>
791 </repeat>
792 </repeat>
793 <repeat name="group">
794 <param name="group_name" value="Other group"/>
795 <repeat name="format">
796 <conditional name="formatChoice">
797 <param name="format_select" value="gtf"/>
798 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
799 <param name="track_color" value="#000000"/>
800 </conditional>
801 </repeat>
802 </repeat>
803 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">
804 <!-- Check myHub structure -->
805 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_both/myHub/genomes.txt"/>
806 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_both/myHub/Dbia3.html"/>
807 <!-- Email could be different, but we need to ensure we still have the email line -->
808 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_both/myHub/hub.txt"
809 lines_diff="2">
810 <assert_contents>
811 <has_text text="email"/>
812 </assert_contents>
813 </extra_files>
814 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
815 </extra_files>
816 <extra_files type="file" name="myHub/Dbia3/description.html"
817 value="two_groups_one_track_both/myHub/Dbia3/description.html"/>
818
819 <!-- Check tracks exist -->
820 <!-- First group -->
821 <extra_files type="file"
822 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
823 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
824 compare="sim_size"
825 />
826
827 <!-- Second group -->
828 <extra_files type="file"
829 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
830 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
831 compare="sim_size"
832 />
833 <!-- Check the groups.txt exists and is properly populated -->
834 </output>
835 </test>
836
837 <!-- Test with two groups and multiple tracks in both -->
838 <test>
839 <param name="genome_name" value="Dbia3"/>
840 <param name="fasta_file" value="common/dbia3.fa"/>
841 <repeat name="group">
842 <param name="group_name" value="Default group"/>
843 <repeat name="format">
844 <conditional name="formatChoice">
845 <param name="format_select" value="bigwig"/>
846 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
847 <param name="track_color" value="#000000"/>
848 </conditional>
849 </repeat>
850 <repeat name="format">
851 <conditional name="formatChoice">
852 <param name="format_select" value="bam"/>
853 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
854 <param name="track_color" value="#000000"/>
855 </conditional>
856 </repeat>
857 </repeat>
858 <repeat name="group">
859 <param name="group_name" value="Other group"/>
860 <repeat name="format">
861 <conditional name="formatChoice">
862 <param name="format_select" value="gtf"/>
863 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
864 <param name="track_color" value="#000000"/>
865 </conditional>
866 </repeat>
867 <repeat name="format">
868 <conditional name="formatChoice">
869 <param name="format_select" value="gff3"/>
870 <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/>
871 <param name="track_color" value="#000000"/>
872 </conditional>
873 </repeat>
874 </repeat>
875 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">
876 <!-- Check myHub structure -->
877 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_multiple_tracks/myHub/genomes.txt"/>
878 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_multiple_tracks/myHub/Dbia3.html"/>
879 <!-- Email could be different, but we need to ensure we still have the email line -->
880 <extra_files type="file" name="myHub/hub.txt" value="two_groups_multiple_tracks/myHub/hub.txt"
881 lines_diff="2">
882 <assert_contents>
883 <has_text text="email"/>
884 </assert_contents>
885 </extra_files>
886 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
887 </extra_files>
888 <extra_files type="file" name="myHub/Dbia3/description.html"
889 value="two_groups_multiple_tracks/myHub/Dbia3/description.html"/>
890
891 <!-- Check tracks exist -->
892 <!-- First group -->
893 <extra_files type="file"
894 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
895 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
896 compare="sim_size"
897 />
898 <extra_files type="file"
899 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
900 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
901 compare="sim_size"
902 />
903 <extra_files type="file"
904 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
905 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
906 compare="sim_size"
907 />
908
909 <!-- Second group -->
910 <extra_files type="file"
911 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
912 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
913 compare="sim_size"
914 />
915 <extra_files type="file"
916 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
917 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
918 compare="sim_size"
919 />
920 <!-- Check the groups.txt exists and is properly populated -->
921 </output>
922 </test>
923
924 <!-- Test default color in a track -->
925 <test>
926 <param name="genome_name" value="Dbia3"/>
927 <param name="fasta_file" value="common/dbia3.fa"/>
928 <repeat name="group">
929 <param name="group_name" value="Default group"/>
930 <repeat name="format">
931 <conditional name="formatChoice">
932 <param name="format_select" value="bam"/>
933 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
934 <param name="track_color" value="#000000"/>
935 </conditional>
936 </repeat>
937 </repeat>
938 <output name="output" file="default_color/default_color_trackhub.html">
939 <!-- Verify trackDb.txt contains the color 0,0,0 -->
940 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="default_color/myHub/Dbia3/trackDb.txt">
941 <assert_contents>
942 <has_text text="color 0,0,0"/>
943 </assert_contents>
944 </extra_files>
945
946 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
947 </output>
948 </test>
949
950 <!-- Test changed color in a track -->
951 <test>
952 <param name="genome_name" value="Dbia3"/>
953 <param name="fasta_file" value="common/dbia3.fa"/>
954 <repeat name="group">
955 <param name="group_name" value="Default group"/>
956 <repeat name="format">
957 <conditional name="formatChoice">
958 <param name="format_select" value="bam"/>
959 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
960 <param name="track_color" value="#8064a2"/>
961 </conditional>
962 </repeat>
963 </repeat>
964 <output name="output" file="changed_color/changed_color_trackhub.html">
965 <!-- Verify trackDb.txt contains the color 128,100,162 -->
966 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="changed_color/myHub/Dbia3/trackDb.txt">
967 <assert_contents>
968 <has_text text="color 128,100,162"/>
969 </assert_contents>
970 </extra_files>
971
972 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
973 </output>
974 </test>
975
976 <!-- Test for StringTie Chromosome end coordinates -->
977 <test>
978 <param name="genome_name" value="Dbia3"/>
979 <param name="fasta_file" value="common/dbia3.fa"/>
980 <repeat name="group">
981 <param name="group_name" value="Default group"/>
982 <repeat name="format">
983 <conditional name="formatChoice">
984 <param name="format_select" value="gtf"/>
985 <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>
986 <param name="track_color" value="#000000"/>
987 </conditional>
988 </repeat>
989 </repeat>
990 <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">
991 <extra_files type="file"
992 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
993 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
994 compare="sim_size"
995 />
996
997 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
998 </output>
999 </test>
1000
1001 <!-- Test for big files? -->
1002
1003 <!-- Find tests that should fail -->
1004
371 </tests> 1005 </tests>
372 1006
373 <help> 1007 <help>
374 This Galaxy tool permits to prepare your files to be ready for 1008 This Galaxy tool permits to prepare your files to be ready for
375 Assembly Hub visualization. 1009 Assembly Hub visualization.