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planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
author yating-l
date Wed, 21 Dec 2016 12:13:04 -0500
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1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.0">
2 <description>
3 This Galaxy tool permits to prepare your files to be ready for
4 Assembly Hub visualization.
5 </description>
6
7 <requirements>
8 <!-- Conda dependencies -->
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>
27 </requirements>
28
29 <stdio>
30 <regex match="^pass1"
31 source="stderr"
32 level="log"
33 description="bedToBigBed"/>
34 <!-- TODO: Add the case pass1 and 0 chroms -->
35 <!-- TODO: Add the case pass2 and 0 records or 0 fields -->
36 </stdio>
37
38 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
39 <command detect_errors="exit_code"><![CDATA[
40 mkdir -p $output.extra_files_path;
41
42 python $__tool_directory__/hubArchiveCreator.py
43
44 ## Ask the user to enter the genome name
45 --genome_name '$genome_name'
46
47 #import json
48
49 #set global data_parameter_dict = {}
50
51 ## Function to retrieve the data of the inputs
52 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})
53 #set false_path = str($input_to_prepare)
54 #set name = $input_to_prepare.name
55
56 #set data_dict = {"name": $name}
57 #silent data_dict.update($extra_data_dict)
58
59 ## Add the ordering by taking the tool form indexes
60 #silent $data_dict.update({"order_index": $order_index})
61
62 #silent $data_parameter_dict.update({$false_path: $data_dict})
63
64 #end def
65
66
67 ## Get the number of digits from tracks, to have a unique integer from group index and track index
68
69 #set temp_max_digit = 0
70
71 #for $g in $group
72 #if len($g.format) > $temp_max_digit
73 #silent temp_max_digit = len($g.format)
74 #end if
75 #end for
76
77 #set nb_digits_max_track = len(str($temp_max_digit))
78
79 ## END Get the number of digits
80
81 #for $i_g, $g in enumerate( $group )
82 #for $i, $f in enumerate( $g.format )
83 ## Create the order index using index_group+1 concatenated with index_track
84 #set index_group_final = str($i_g + 1)
85 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
86
87 ## For each format, we have a few mandatory fields we store in a dict
88 #set track_color = str($f.formatChoice.track_color)
89 #set group_name = str($g.group_name)
90
91 #set extra_data_dict = {"track_color": $track_color,
92 "group_name": $group_name}
93
94 #if $f.formatChoice.format_select == "bam"
95 --bam $f.formatChoice.BAM
96 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
97
98 ## Add Bam format specific fields
99 #silent extra_data_dict.update({"index": $bam_index})
100
101 #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict)
102 #end if
103 #if $f.formatChoice.format_select == "bed"
104 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
105 --bed $f.formatChoice.bedChoice.BED
106 #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final,
107 extra_data_dict)
108 #end if
109 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
110 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
111 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
112 extra_data_dict)
113 #end if
114 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
115 --bedSpliceJunctions $f.formatChoice.bedChoice.Bed_splice_junctions
116 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
117 extra_data_dict)
118 #end if
119 #end if
120 #if $f.formatChoice.format_select == "psl"
121 --psl $f.formatChoice.PSL
122 #silent $prepare_json($f.formatChoice.PSL, $index_track_final,
123 extra_data_dict)
124 #end if
125 #if $f.formatChoice.format_select == "bigwig"
126 --bigwig $f.formatChoice.BIGWIG
127 #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final,
128 extra_data_dict)
129 #end if
130 #if $f.formatChoice.format_select == "gff3"
131 --gff3 $f.formatChoice.GFF3
132 #silent $prepare_json($f.formatChoice.GFF3, $index_track_final,
133 extra_data_dict)
134 #end if
135 #if $f.formatChoice.format_select == "gtf"
136 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
137 --gtf $f.formatChoice.GTF
138 #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
139 extra_data_dict)
140 #end if
141 #end for
142 #end for
143
144 ## We combine the fasta file dataset name with his false path in a JSON object
145 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
146 -f '$fasta_json'
147
148 ## Dump the final json
149 #set all_data_json = json.dumps($data_parameter_dict)
150
151 --data_json '$all_data_json'
152
153 ## Retrieve the user email
154 --user_email $__user_email__
155
156 -d $__tool_directory__
157
158 -e $output.extra_files_path
159
160 $advanced_options.debug_mode
161
162 -o $output;
163
164 ]]></command>
165
166 <inputs>
167 <param
168 name="genome_name"
169 type="text"
170 size="30"
171 value="unknown"
172 label="UCSC Genome Browser assembly ID"
173 />
174 <param
175 format="fasta"
176 name="fasta_file"
177 type="data"
178 label="Reference genome"
179 />
180 <repeat name="group" title="New group">
181 <param type="text" name="group_name" label="Group name" value="Default group"/>
182 <repeat name="format" title="New track">
183 <conditional name="formatChoice">
184 <param name="format_select" type="select" label="Format">
185 <option value="bam" selected="true">BAM</option>
186 <option value="bed">BED</option>
187 <option value="psl">PSL</option>
188 <option value="bigwig">BIGWIG</option>
189 <option value="gff3">GFF3</option>
190 <option value="gtf">GTF</option>
191 </param>
192
193 <when value="bam">
194 <param
195 format="bam"
196 name="BAM"
197 type="data"
198 label="BAM File"
199 />
200 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
201 <param name="track_color" type="color" label="Track color" value="#000000">
202 <sanitizer>
203 <valid initial="string.letters,string.digits">
204 <add value="#"/>
205 </valid>
206 </sanitizer>
207 </param>
208 </when>
209 <when value="bed">
210 <conditional name="bedChoice">
211 <param name="bed_select" type="select" label="Bed Choice">
212 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
213 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
214 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
215 </param>
216 <when value="bed_generic">
217 <param
218 format="bed"
219 name="BED"
220 type="data"
221 label="Generic Bed File Choice"
222 />
223
224 </when>
225 <when value="bed_simple_repeats_option">
226 <param
227 format="bed"
228 name="BED_simple_repeats"
229 type="data"
230 label="Bed Simple Repeats (Bed4+12) File"
231 />
232 </when>
233 <when value="bed_splice_junctions_option">
234 <param
235 format="bed"
236 name="BED_splice_junctions"
237 type="data"
238 label="Bed Splice Junctions (Bed12+1) File"
239 />
240 </when>
241 </conditional>
242 <param name="track_color" type="color" label="Track color" value="#000000">
243 <sanitizer>
244 <valid initial="string.letters,string.digits">
245 <add value="#"/>
246 </valid>
247 </sanitizer>
248 </param>
249 </when>
250 <when value="psl">
251 <param
252 format="psl"
253 name="PSL"
254 type="data"
255 label="PSL File"
256 />
257 <param name="track_color" type="color" label="Track color" value="#000000">
258 <sanitizer>
259 <valid initial="string.letters,string.digits">
260 <add value="#"/>
261 </valid>
262 </sanitizer>
263 </param>
264 </when>
265 <when value="bigwig">
266 <param
267 format="bigwig"
268 name="BIGWIG"
269 type="data"
270 label="BIGWIG File"
271 />
272 <param name="track_color" type="color" label="Track color" value="#000000">
273 <sanitizer>
274 <valid initial="string.letters,string.digits">
275 <add value="#"/>
276 </valid>
277 </sanitizer>
278 </param>
279 </when>
280 <when value="gff3">
281 <param
282 format="gff3"
283 name="GFF3"
284 type="data"
285 label="GFF3 File"
286 />
287 <param name="track_color" type="color" label="Track color" value="#000000">
288 <sanitizer>
289 <valid initial="string.letters,string.digits">
290 <add value="#"/>
291 </valid>
292 </sanitizer>
293 </param>
294 </when>
295 <when value="gtf">
296 <param
297 format="gtf"
298 name="GTF"
299 type="data"
300 label="GTF File"
301 />
302 <param name="track_color" type="color" label="Track color" value="#000000">
303 <sanitizer>
304 <valid initial="string.letters,string.digits">
305 <add value="#"/>
306 </valid>
307 </sanitizer>
308 </param>
309 </when>
310 </conditional>
311 </repeat>
312 </repeat>
313 <conditional name="advanced_options">
314 <param name="advanced_options_selector" type="select" label="Advanced options">
315 <option value="off" selected="true">Hide advanced options</option>
316 <option value="on">Display advanced options</option>
317 </param>
318 <!-- TODO: Avoid redundancy here -->
319 <when value="on">
320 <param name="debug_mode" type="boolean"
321 label="Activate debug mode" checked="false"
322 truevalue="--debug_mode" falsevalue="">
323 <help>
324 Use this option if you are a G-OnRamp developer
325 </help>
326 </param>
327 </when>
328 <when value="off">
329 <param name="debug_mode" type="hidden"
330 value="">
331 </param>
332 </when>
333 </conditional>
334 </inputs>
335
336 <outputs>
337 <data format="trackhub" name="output"/>
338 </outputs>
339
340 <tests>
341 <!-- Test with only the fasta file -->
342 <test>
343 <param name="genome_name" value="Dbia3"/>
344 <param name="fasta_file" value="common/dbia3.fa"/>
345 <output name="output" file="only_genome/only_genome.html">
346 <extra_files type="file" name="__main__.log" value="only_genome/__main__.log" />
347 <extra_files type="file" name="myHub/genomes.txt" value="only_genome/myHub/genomes.txt" />
348 <extra_files type="file" name="myHub/Dbia3.html" value="only_genome/myHub/Dbia3.html"/>
349 <!-- Email could be different, but we need to ensure we still have the email line -->
350 <extra_files type="file" name="myHub/hub.txt" value="only_genome/myHub/hub.txt" lines_diff="2">
351 <assert_contents>
352 <has_text text="email"/>
353 </assert_contents>
354 </extra_files>
355 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
356 </extra_files>
357 <extra_files type="file" name="myHub/Dbia3/description.html" value="only_genome/myHub/Dbia3/description.html"/>
358 </output>
359 </test>
360
361 <!-- Test with Bam -->
362 <test>
363 <param name="genome_name" value="Dbia3"/>
364 <param name="fasta_file" value="common/dbia3.fa"/>
365 <repeat name="group">
366 <param name="group_name" value="Default group"/>
367 <repeat name="format">
368 <conditional name="formatChoice">
369 <param name="format_select" value="bam"/>
370 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
371 <param name="track_color" value="#000000"/>
372 </conditional>
373 </repeat>
374 </repeat>
375 <output name="output" file="bam/bam.html">
376 <!-- Verify tracks folder contains bam and bai -->
377 <extra_files type="file"
378 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
379 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
380 compare="sim_size"
381 />
382 <extra_files type="file"
383 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
384 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
385 compare="sim_size"
386 />
387 <!-- Verify trackDb.txt contains the basic fields for a bam -->
388 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="bam/myHub/Dbia3/trackDb.txt">
389 <assert_contents>
390 <has_text text="track"/>
391 <has_text text="longLabel"/>
392 <has_text text="shortLabel"/>
393 <has_text text="bigDataUrl"/>
394 <has_text text="type"/>
395 <has_text text="visibility"/>
396 <has_text text="thickDrawItem"/>
397 <has_text text="priority"/>
398 <has_text text="color"/>
399 <has_text text="group"/>
400 </assert_contents>
401 </extra_files>
402 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
403 </output>
404 </test>
405
406 <!-- Test with Bed Generic -->
407 <test>
408 <param name="genome_name" value="Dbia3"/>
409 <param name="fasta_file" value="common/dbia3.fa"/>
410 <repeat name="group">
411 <param name="group_name" value="Default group"/>
412 <repeat name="format">
413 <conditional name="formatChoice">
414 <param name="format_select" value="bed" />
415 <conditional name="bedChoice">
416 <param name="bed_select" value="bed_generic"/>
417 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
418 <param name="track_color" value="#000000"/>
419 </conditional>
420 </conditional>
421 </repeat>
422 </repeat>
423 <output name="output" file="bed_generic/bed_generic.html">
424 <!-- Verify tracks folder contains bam and bai -->
425 <extra_files type="file"
426 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
427 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
428 compare="sim_size"
429 />
430 </output>
431 </test>
432
433 <!-- Test with Bed Simple repeat -->
434 <test>
435 <param name="genome_name" value="Dbia3"/>
436 <param name="fasta_file" value="common/dbia3.fa"/>
437 <repeat name="group">
438 <param name="group_name" value="Default group"/>
439 <repeat name="format">
440 <conditional name="formatChoice">
441 <param name="format_select" value="bed" />
442 <conditional name="bedChoice">
443 <param name="bed_select" value="bed_simple_repeats_option"/>
444 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
445 <param name="track_color" value="#000000"/>
446 </conditional>
447 </conditional>
448 </repeat>
449 </repeat>
450 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
451 <!-- Verify tracks folder contains bam and bai -->
452 <extra_files type="file"
453 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
454 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
455 compare="sim_size"
456 />
457 </output>
458 </test>
459
460
461 <!-- Test with Psl -->
462 <test>
463 <param name="genome_name" value="Dbia3"/>
464 <param name="fasta_file" value="common/dbia3.fa"/>
465 <repeat name="group">
466 <param name="group_name" value="Default group"/>
467 <repeat name="format">
468 <conditional name="formatChoice">
469 <param name="format_select" value="psl"/>
470 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
471 <param name="track_color" value="#000000"/>
472 </conditional>
473 </repeat>
474 </repeat>
475 <output name="output" file="psl/psl_trackhub.html">
476 <!-- Verify tracks folder contains bam and bai -->
477 <extra_files type="file"
478 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
479 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
480 compare="sim_size"
481 />
482 <!-- Verify trackDb.txt contains the basic fields for a bam -->
483 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
484 </output>
485 </test>
486
487 <!-- Test with BigWig -->
488 <test>
489 <param name="genome_name" value="Dbia3"/>
490 <param name="fasta_file" value="common/dbia3.fa"/>
491 <repeat name="group">
492 <param name="group_name" value="Default group"/>
493 <repeat name="format">
494 <conditional name="formatChoice">
495 <param name="format_select" value="bigwig"/>
496 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
497 <param name="track_color" value="#000000"/>
498 </conditional>
499 </repeat>
500 </repeat>
501 <output name="output" file="bigwig/bigwig.html">
502 <!-- Verify tracks folder contains bam and bai -->
503 <extra_files type="file"
504 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
505 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
506 compare="sim_size"
507 />
508 <!-- Verify trackDb.txt contains the basic fields for a bam -->
509 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
510 </output>
511 </test>
512
513 <!-- Test with GFF3 -->
514 <test>
515 <param name="genome_name" value="Dbia3"/>
516 <param name="fasta_file" value="common/dbia3.fa"/>
517 <repeat name="group">
518 <param name="group_name" value="Default group"/>
519 <repeat name="format">
520 <conditional name="formatChoice">
521 <param name="format_select" value="gff3"/>
522 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
523 <param name="track_color" value="#000000"/>
524 </conditional>
525 </repeat>
526 </repeat>
527 <output name="output" file="gff3/gff3_trackhub.html">
528 <!-- Verify tracks folder contains bam and bai -->
529 <extra_files type="file"
530 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
531 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
532 compare="sim_size"
533 />
534 <!-- Verify trackDb.txt contains the basic fields for a bam -->
535 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
536 </output>
537 </test>
538
539 <!-- Test with GTF -->
540 <test>
541 <param name="genome_name" value="Dbia3"/>
542 <param name="fasta_file" value="common/dbia3.fa"/>
543 <repeat name="group">
544 <param name="group_name" value="Default group"/>
545 <repeat name="format">
546 <conditional name="formatChoice">
547 <param name="format_select" value="gtf"/>
548 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
549 <param name="track_color" value="#000000"/>
550 </conditional>
551 </repeat>
552 </repeat>
553 <output name="output" file="gtf/gtf_trackhub.html">
554 <!-- Verify tracks folder contains bam and bai -->
555 <extra_files type="file"
556 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
557 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
558 compare="sim_size"
559 />
560 <!-- Verify trackDb.txt contains the basic fields for a bam -->
561 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
562 </output>
563 </test>
564
565 <!-- Test with one group and multiple tracks -->
566 <test>
567 <param name="genome_name" value="Dbia3"/>
568 <param name="fasta_file" value="common/dbia3.fa"/>
569 <repeat name="group">
570 <param name="group_name" value="Default group"/>
571 <repeat name="format">
572 <conditional name="formatChoice">
573 <param name="format_select" value="gtf"/>
574 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
575 <param name="track_color" value="#000000"/>
576 </conditional>
577 </repeat>
578 <repeat name="format">
579 <conditional name="formatChoice">
580 <param name="format_select" value="gff3"/>
581 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
582 <param name="track_color" value="#000000"/>
583 </conditional>
584 </repeat>
585 </repeat>
586 <output name="output" file="gtf_gff/gtf_gff_trackhub.html">
587 <!-- verify tracks folder contains bam and bai -->
588 <extra_files type="file"
589 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
590 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
591 compare="sim_size"
592 />
593 <extra_files type="file"
594 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
595 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
596 compare="sim_size"
597 />
598 <!-- verify trackdb.txt contains the basic fields for a bam -->
599 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
600 </output>
601 </test>
602
603 <!-- Test with one group and all the supported datatypes on 10/04/2016 -->
604 <test>
605 <param name="genome_name" value="Dbia3"/>
606 <param name="fasta_file" value="common/dbia3.fa"/>
607 <repeat name="group">
608 <param name="group_name" value="Default group"/>
609 <repeat name="format">
610 <conditional name="formatChoice">
611 <param name="format_select" value="bam"/>
612 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
613 <param name="track_color" value="#000000"/>
614 </conditional>
615 </repeat>
616 <repeat name="format">
617 <conditional name="formatChoice">
618 <param name="format_select" value="bed"/>
619 <conditional name="bedChoice">
620 <param name="bed_select" value="bed_generic"/>
621 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
622 <param name="track_color" value="#000000"/>
623 </conditional>
624 </conditional>
625 </repeat>
626 <repeat name="format">
627 <conditional name="formatChoice">
628 <param name="format_select" value="bed"/>
629 <conditional name="bedChoice">
630 <param name="bed_select" value="bed_simple_repeats_option"/>
631 <param name="BED_simple_repeats" ftype="bed"
632 value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
633 <param name="track_color" value="#000000"/>
634 </conditional>
635 </conditional>
636 </repeat>
637 <repeat name="format">
638 <conditional name="formatChoice">
639 <param name="format_select" value="psl"/>
640 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
641 <param name="track_color" value="#000000"/>
642 </conditional>
643 </repeat>
644 <repeat name="format">
645 <conditional name="formatChoice">
646 <param name="format_select" value="bigwig"/>
647 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
648 <param name="track_color" value="#000000"/>
649 </conditional>
650 </repeat>
651 <repeat name="format">
652 <conditional name="formatChoice">
653 <param name="format_select" value="gff3"/>
654 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
655 <param name="track_color" value="#000000"/>
656 </conditional>
657 </repeat>
658 <repeat name="format">
659 <conditional name="formatChoice">
660 <param name="format_select" value="gtf"/>
661 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
662 <param name="track_color" value="#000000"/>
663 </conditional>
664 </repeat>
665 </repeat>
666 <output name="output" file="all_datatypes/all_datatypes_trackhub.html">
667 <!-- verify tracks folder contains all the files -->
668 <extra_files type="file"
669 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
670 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
671 compare="sim_size"
672 />
673 <extra_files type="file"
674 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
675 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
676 compare="sim_size"
677 />
678 <extra_files type="file"
679 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
680 value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
681 compare="sim_size"
682 />
683 <extra_files type="file"
684 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
685 value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
686 compare="sim_size"
687 />
688 <extra_files type="file"
689 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
690 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb"
691 compare="sim_size"
692 />
693 <extra_files type="file"
694 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
695 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
696 compare="sim_size"
697 />
698 <extra_files type="file"
699 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
700 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
701 compare="sim_size"
702 />
703 <extra_files type="file"
704 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
705 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
706 compare="sim_size"
707 />
708 <!-- verify trackdb.txt contains the basic fields for a bam -->
709 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
710 </output>
711 </test>
712
713 <!-- Test with two groups and no tracks -->
714 <test>
715 <param name="genome_name" value="Dbia3"/>
716 <param name="fasta_file" value="common/dbia3.fa"/>
717 <repeat name="group">
718 <param name="group_name" value="Default group"/>
719 </repeat>
720 <repeat name="group">
721 <param name="group_name" value="Other group"/>
722 </repeat>
723 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
724 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_no_track/myHub/genomes.txt"/>
725 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_no_track/myHub/Dbia3.html"/>
726 <!-- Email could be different, but we need to ensure we still have the email line -->
727 <extra_files type="file" name="myHub/hub.txt" value="two_groups_no_track/myHub/hub.txt" lines_diff="2">
728 <assert_contents>
729 <has_text text="email"/>
730 </assert_contents>
731 </extra_files>
732 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
733 </extra_files>
734 <extra_files type="file" name="myHub/Dbia3/description.html"
735 value="two_groups_no_track/myHub/Dbia3/description.html"/>
736 </output>
737 </test>
738
739 <!-- Test with two groups and one track in first -->
740 <test>
741 <param name="genome_name" value="Dbia3"/>
742 <param name="fasta_file" value="common/dbia3.fa"/>
743 <repeat name="group">
744 <param name="group_name" value="Default group"/>
745 <repeat name="format">
746 <conditional name="formatChoice">
747 <param name="format_select" value="bigwig"/>
748 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
749 <param name="track_color" value="#000000"/>
750 </conditional>
751 </repeat>
752 </repeat>
753 <repeat name="group">
754 <param name="group_name" value="Other group"/>
755 </repeat>
756 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">
757 <!-- Check myHub structure -->
758 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_first/myHub/genomes.txt"/>
759 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_first/myHub/Dbia3.html"/>
760 <!-- Email could be different, but we need to ensure we still have the email line -->
761 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_first/myHub/hub.txt" lines_diff="2">
762 <assert_contents>
763 <has_text text="email"/>
764 </assert_contents>
765 </extra_files>
766 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
767 </extra_files>
768 <extra_files type="file" name="myHub/Dbia3/description.html"
769 value="two_groups_one_track_first/myHub/Dbia3/description.html"/>
770
771 <!-- Check tracks exist -->
772 <extra_files type="file"
773 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
774 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
775 compare="sim_size"
776 />
777
778 <!-- Check the groups.txt exists and is properly populated -->
779 </output>
780 </test>
781
782 <!-- Test with two groups and one track in both -->
783 <test>
784 <param name="genome_name" value="Dbia3"/>
785 <param name="fasta_file" value="common/dbia3.fa"/>
786 <repeat name="group">
787 <param name="group_name" value="Default group"/>
788 <repeat name="format">
789 <conditional name="formatChoice">
790 <param name="format_select" value="bigwig"/>
791 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
792 <param name="track_color" value="#000000"/>
793 </conditional>
794 </repeat>
795 </repeat>
796 <repeat name="group">
797 <param name="group_name" value="Other group"/>
798 <repeat name="format">
799 <conditional name="formatChoice">
800 <param name="format_select" value="gtf"/>
801 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
802 <param name="track_color" value="#000000"/>
803 </conditional>
804 </repeat>
805 </repeat>
806 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">
807 <!-- Check myHub structure -->
808 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_both/myHub/genomes.txt"/>
809 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_both/myHub/Dbia3.html"/>
810 <!-- Email could be different, but we need to ensure we still have the email line -->
811 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_both/myHub/hub.txt"
812 lines_diff="2">
813 <assert_contents>
814 <has_text text="email"/>
815 </assert_contents>
816 </extra_files>
817 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
818 </extra_files>
819 <extra_files type="file" name="myHub/Dbia3/description.html"
820 value="two_groups_one_track_both/myHub/Dbia3/description.html"/>
821
822 <!-- Check tracks exist -->
823 <!-- First group -->
824 <extra_files type="file"
825 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
826 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
827 compare="sim_size"
828 />
829
830 <!-- Second group -->
831 <extra_files type="file"
832 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
833 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
834 compare="sim_size"
835 />
836 <!-- Check the groups.txt exists and is properly populated -->
837 </output>
838 </test>
839
840 <!-- Test with two groups and multiple tracks in both -->
841 <test>
842 <param name="genome_name" value="Dbia3"/>
843 <param name="fasta_file" value="common/dbia3.fa"/>
844 <repeat name="group">
845 <param name="group_name" value="Default group"/>
846 <repeat name="format">
847 <conditional name="formatChoice">
848 <param name="format_select" value="bigwig"/>
849 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
850 <param name="track_color" value="#000000"/>
851 </conditional>
852 </repeat>
853 <repeat name="format">
854 <conditional name="formatChoice">
855 <param name="format_select" value="bam"/>
856 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
857 <param name="track_color" value="#000000"/>
858 </conditional>
859 </repeat>
860 </repeat>
861 <repeat name="group">
862 <param name="group_name" value="Other group"/>
863 <repeat name="format">
864 <conditional name="formatChoice">
865 <param name="format_select" value="gtf"/>
866 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
867 <param name="track_color" value="#000000"/>
868 </conditional>
869 </repeat>
870 <repeat name="format">
871 <conditional name="formatChoice">
872 <param name="format_select" value="gff3"/>
873 <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/>
874 <param name="track_color" value="#000000"/>
875 </conditional>
876 </repeat>
877 </repeat>
878 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">
879 <!-- Check myHub structure -->
880 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_multiple_tracks/myHub/genomes.txt"/>
881 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_multiple_tracks/myHub/Dbia3.html"/>
882 <!-- Email could be different, but we need to ensure we still have the email line -->
883 <extra_files type="file" name="myHub/hub.txt" value="two_groups_multiple_tracks/myHub/hub.txt"
884 lines_diff="2">
885 <assert_contents>
886 <has_text text="email"/>
887 </assert_contents>
888 </extra_files>
889 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
890 </extra_files>
891 <extra_files type="file" name="myHub/Dbia3/description.html"
892 value="two_groups_multiple_tracks/myHub/Dbia3/description.html"/>
893
894 <!-- Check tracks exist -->
895 <!-- First group -->
896 <extra_files type="file"
897 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
898 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
899 compare="sim_size"
900 />
901 <extra_files type="file"
902 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
903 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
904 compare="sim_size"
905 />
906 <extra_files type="file"
907 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
908 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
909 compare="sim_size"
910 />
911
912 <!-- Second group -->
913 <extra_files type="file"
914 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
915 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
916 compare="sim_size"
917 />
918 <extra_files type="file"
919 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
920 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
921 compare="sim_size"
922 />
923 <!-- Check the groups.txt exists and is properly populated -->
924 </output>
925 </test>
926
927 <!-- Test default color in a track -->
928 <test>
929 <param name="genome_name" value="Dbia3"/>
930 <param name="fasta_file" value="common/dbia3.fa"/>
931 <repeat name="group">
932 <param name="group_name" value="Default group"/>
933 <repeat name="format">
934 <conditional name="formatChoice">
935 <param name="format_select" value="bam"/>
936 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
937 <param name="track_color" value="#000000"/>
938 </conditional>
939 </repeat>
940 </repeat>
941 <output name="output" file="default_color/default_color_trackhub.html">
942 <!-- Verify trackDb.txt contains the color 0,0,0 -->
943 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="default_color/myHub/Dbia3/trackDb.txt">
944 <assert_contents>
945 <has_text text="color 0,0,0"/>
946 </assert_contents>
947 </extra_files>
948
949 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
950 </output>
951 </test>
952
953 <!-- Test changed color in a track -->
954 <test>
955 <param name="genome_name" value="Dbia3"/>
956 <param name="fasta_file" value="common/dbia3.fa"/>
957 <repeat name="group">
958 <param name="group_name" value="Default group"/>
959 <repeat name="format">
960 <conditional name="formatChoice">
961 <param name="format_select" value="bam"/>
962 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
963 <param name="track_color" value="#8064a2"/>
964 </conditional>
965 </repeat>
966 </repeat>
967 <output name="output" file="changed_color/changed_color_trackhub.html">
968 <!-- Verify trackDb.txt contains the color 128,100,162 -->
969 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="changed_color/myHub/Dbia3/trackDb.txt">
970 <assert_contents>
971 <has_text text="color 128,100,162"/>
972 </assert_contents>
973 </extra_files>
974
975 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
976 </output>
977 </test>
978
979 <!-- Test for StringTie Chromosome end coordinates -->
980 <test>
981 <param name="genome_name" value="Dbia3"/>
982 <param name="fasta_file" value="common/dbia3.fa"/>
983 <repeat name="group">
984 <param name="group_name" value="Default group"/>
985 <repeat name="format">
986 <conditional name="formatChoice">
987 <param name="format_select" value="gtf"/>
988 <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>
989 <param name="track_color" value="#000000"/>
990 </conditional>
991 </repeat>
992 </repeat>
993 <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">
994 <extra_files type="file"
995 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
996 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
997 compare="sim_size"
998 />
999
1000 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
1001 </output>
1002 </test>
1003
1004 <!-- Test for big files? -->
1005
1006 <!-- Find tests that should fail -->
1007
1008 </tests>
1009
1010 <help>
1011 This Galaxy tool permits to prepare your files to be ready for
1012 Assembly Hub visualization.
1013 </help>
1014 </tool>