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planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
author yating-l
date Thu, 22 Dec 2016 17:53:00 -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 #end if
115 #if $f.formatChoice.format_select == "psl"
116 --psl $f.formatChoice.PSL
117 #silent $prepare_json($f.formatChoice.PSL, $index_track_final,
118 extra_data_dict)
119 #end if
120 #if $f.formatChoice.format_select == "bigwig"
121 --bigwig $f.formatChoice.BIGWIG
122 #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final,
123 extra_data_dict)
124 #end if
125 #if $f.formatChoice.format_select == "gff3"
126 --gff3 $f.formatChoice.GFF3
127 #silent $prepare_json($f.formatChoice.GFF3, $index_track_final,
128 extra_data_dict)
129 #end if
130 #if $f.formatChoice.format_select == "gtf"
131 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
132 --gtf $f.formatChoice.GTF
133 #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
134 extra_data_dict)
135 #end if
136 #end for
137 #end for
138
139 ## We combine the fasta file dataset name with his false path in a JSON object
140 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
141 -f '$fasta_json'
142
143 ## Dump the final json
144 #set all_data_json = json.dumps($data_parameter_dict)
145
146 --data_json '$all_data_json'
147
148 ## Retrieve the user email
149 --user_email $__user_email__
150
151 -d $__tool_directory__
152
153 -e $output.extra_files_path
154
155 $advanced_options.debug_mode
156
157 -o $output;
158
159 ]]></command>
160
161 <inputs>
162 <param
163 name="genome_name"
164 type="text"
165 size="30"
166 value="unknown"
167 label="UCSC Genome Browser assembly ID"
168 />
169 <param
170 format="fasta"
171 name="fasta_file"
172 type="data"
173 label="Reference genome"
174 />
175 <repeat name="group" title="New group">
176 <param type="text" name="group_name" label="Group name" value="Default group"/>
177 <repeat name="format" title="New track">
178 <conditional name="formatChoice">
179 <param name="format_select" type="select" label="Format">
180 <option value="bam" selected="true">BAM</option>
181 <option value="bed">BED</option>
182 <option value="psl">PSL</option>
183 <option value="bigwig">BIGWIG</option>
184 <option value="gff3">GFF3</option>
185 <option value="gtf">GTF</option>
186 </param>
187
188 <when value="bam">
189 <param
190 format="bam"
191 name="BAM"
192 type="data"
193 label="BAM File"
194 />
195 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
196 <param name="track_color" type="color" label="Track color" value="#000000">
197 <sanitizer>
198 <valid initial="string.letters,string.digits">
199 <add value="#"/>
200 </valid>
201 </sanitizer>
202 </param>
203 </when>
204 <when value="bed">
205 <conditional name="bedChoice">
206 <param name="bed_select" type="select" label="Bed Choice">
207 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
208 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
209 </param>
210 <when value="bed_generic">
211 <param
212 format="bed"
213 name="BED"
214 type="data"
215 label="Generic Bed File Choice"
216 />
217
218 </when>
219 <when value="bed_simple_repeats_option">
220 <param
221 format="bed"
222 name="BED_simple_repeats"
223 type="data"
224 label="Bed Simple Repeats (Bed4+12) File"
225 />
226 </when>
227 </conditional>
228 <param name="track_color" type="color" label="Track color" value="#000000">
229 <sanitizer>
230 <valid initial="string.letters,string.digits">
231 <add value="#"/>
232 </valid>
233 </sanitizer>
234 </param>
235 </when>
236 <when value="psl">
237 <param
238 format="psl"
239 name="PSL"
240 type="data"
241 label="PSL File"
242 />
243 <param name="track_color" type="color" label="Track color" value="#000000">
244 <sanitizer>
245 <valid initial="string.letters,string.digits">
246 <add value="#"/>
247 </valid>
248 </sanitizer>
249 </param>
250 </when>
251 <when value="bigwig">
252 <param
253 format="bigwig"
254 name="BIGWIG"
255 type="data"
256 label="BIGWIG File"
257 />
258 <param name="track_color" type="color" label="Track color" value="#000000">
259 <sanitizer>
260 <valid initial="string.letters,string.digits">
261 <add value="#"/>
262 </valid>
263 </sanitizer>
264 </param>
265 </when>
266 <when value="gff3">
267 <param
268 format="gff3"
269 name="GFF3"
270 type="data"
271 label="GFF3 File"
272 />
273 <param name="track_color" type="color" label="Track color" value="#000000">
274 <sanitizer>
275 <valid initial="string.letters,string.digits">
276 <add value="#"/>
277 </valid>
278 </sanitizer>
279 </param>
280 </when>
281 <when value="gtf">
282 <param
283 format="gtf"
284 name="GTF"
285 type="data"
286 label="GTF File"
287 />
288 <param name="track_color" type="color" label="Track color" value="#000000">
289 <sanitizer>
290 <valid initial="string.letters,string.digits">
291 <add value="#"/>
292 </valid>
293 </sanitizer>
294 </param>
295 </when>
296 </conditional>
297 </repeat>
298 </repeat>
299 <conditional name="advanced_options">
300 <param name="advanced_options_selector" type="select" label="Advanced options">
301 <option value="off" selected="true">Hide advanced options</option>
302 <option value="on">Display advanced options</option>
303 </param>
304 <!-- TODO: Avoid redundancy here -->
305 <when value="on">
306 <param name="debug_mode" type="boolean"
307 label="Activate debug mode" checked="false"
308 truevalue="--debug_mode" falsevalue="">
309 <help>
310 Use this option if you are a G-OnRamp developer
311 </help>
312 </param>
313 </when>
314 <when value="off">
315 <param name="debug_mode" type="hidden"
316 value="">
317 </param>
318 </when>
319 </conditional>
320 </inputs>
321
322 <outputs>
323 <data format="trackhub" name="output"/>
324 </outputs>
325
326 <tests>
327 <!-- Test with only the fasta file -->
328 <test>
329 <param name="genome_name" value="Dbia3"/>
330 <param name="fasta_file" value="common/dbia3.fa"/>
331 <output name="output" file="only_genome/only_genome.html">
332 <extra_files type="file" name="__main__.log" value="only_genome/__main__.log" />
333 <extra_files type="file" name="myHub/genomes.txt" value="only_genome/myHub/genomes.txt" />
334 <extra_files type="file" name="myHub/Dbia3.html" value="only_genome/myHub/Dbia3.html"/>
335 <!-- Email could be different, but we need to ensure we still have the email line -->
336 <extra_files type="file" name="myHub/hub.txt" value="only_genome/myHub/hub.txt" lines_diff="2">
337 <assert_contents>
338 <has_text text="email"/>
339 </assert_contents>
340 </extra_files>
341 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
342 </extra_files>
343 <extra_files type="file" name="myHub/Dbia3/description.html" value="only_genome/myHub/Dbia3/description.html"/>
344 </output>
345 </test>
346
347 <!-- Test with Bam -->
348 <test>
349 <param name="genome_name" value="Dbia3"/>
350 <param name="fasta_file" value="common/dbia3.fa"/>
351 <repeat name="group">
352 <param name="group_name" value="Default group"/>
353 <repeat name="format">
354 <conditional name="formatChoice">
355 <param name="format_select" value="bam"/>
356 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
357 <param name="track_color" value="#000000"/>
358 </conditional>
359 </repeat>
360 </repeat>
361 <output name="output" file="bam/bam.html">
362 <!-- Verify tracks folder contains bam and bai -->
363 <extra_files type="file"
364 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
365 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
366 compare="sim_size"
367 />
368 <extra_files type="file"
369 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
370 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
371 compare="sim_size"
372 />
373 <!-- Verify trackDb.txt contains the basic fields for a bam -->
374 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="bam/myHub/Dbia3/trackDb.txt">
375 <assert_contents>
376 <has_text text="track"/>
377 <has_text text="longLabel"/>
378 <has_text text="shortLabel"/>
379 <has_text text="bigDataUrl"/>
380 <has_text text="type"/>
381 <has_text text="visibility"/>
382 <has_text text="thickDrawItem"/>
383 <has_text text="priority"/>
384 <has_text text="color"/>
385 <has_text text="group"/>
386 </assert_contents>
387 </extra_files>
388 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
389 </output>
390 </test>
391
392 <!-- Test with Bed Generic -->
393 <test>
394 <param name="genome_name" value="Dbia3"/>
395 <param name="fasta_file" value="common/dbia3.fa"/>
396 <repeat name="group">
397 <param name="group_name" value="Default group"/>
398 <repeat name="format">
399 <conditional name="formatChoice">
400 <param name="format_select" value="bed" />
401 <conditional name="bedChoice">
402 <param name="bed_select" value="bed_generic"/>
403 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
404 <param name="track_color" value="#000000"/>
405 </conditional>
406 </conditional>
407 </repeat>
408 </repeat>
409 <output name="output" file="bed_generic/bed_generic.html">
410 <!-- Verify tracks folder contains bam and bai -->
411 <extra_files type="file"
412 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
413 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
414 compare="sim_size"
415 />
416 </output>
417 </test>
418
419 <!-- Test with Bed Simple repeat -->
420 <test>
421 <param name="genome_name" value="Dbia3"/>
422 <param name="fasta_file" value="common/dbia3.fa"/>
423 <repeat name="group">
424 <param name="group_name" value="Default group"/>
425 <repeat name="format">
426 <conditional name="formatChoice">
427 <param name="format_select" value="bed" />
428 <conditional name="bedChoice">
429 <param name="bed_select" value="bed_simple_repeats_option"/>
430 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
431 <param name="track_color" value="#000000"/>
432 </conditional>
433 </conditional>
434 </repeat>
435 </repeat>
436 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
437 <!-- Verify tracks folder contains bam and bai -->
438 <extra_files type="file"
439 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
440 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
441 compare="sim_size"
442 />
443 </output>
444 </test>
445
446 <!-- Test with Psl -->
447 <test>
448 <param name="genome_name" value="Dbia3"/>
449 <param name="fasta_file" value="common/dbia3.fa"/>
450 <repeat name="group">
451 <param name="group_name" value="Default group"/>
452 <repeat name="format">
453 <conditional name="formatChoice">
454 <param name="format_select" value="psl"/>
455 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
456 <param name="track_color" value="#000000"/>
457 </conditional>
458 </repeat>
459 </repeat>
460 <output name="output" file="psl/psl_trackhub.html">
461 <!-- Verify tracks folder contains bam and bai -->
462 <extra_files type="file"
463 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
464 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
465 compare="sim_size"
466 />
467 <!-- Verify trackDb.txt contains the basic fields for a bam -->
468 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
469 </output>
470 </test>
471
472 <!-- Test with BigWig -->
473 <test>
474 <param name="genome_name" value="Dbia3"/>
475 <param name="fasta_file" value="common/dbia3.fa"/>
476 <repeat name="group">
477 <param name="group_name" value="Default group"/>
478 <repeat name="format">
479 <conditional name="formatChoice">
480 <param name="format_select" value="bigwig"/>
481 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
482 <param name="track_color" value="#000000"/>
483 </conditional>
484 </repeat>
485 </repeat>
486 <output name="output" file="bigwig/bigwig.html">
487 <!-- Verify tracks folder contains bam and bai -->
488 <extra_files type="file"
489 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
490 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
491 compare="sim_size"
492 />
493 <!-- Verify trackDb.txt contains the basic fields for a bam -->
494 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
495 </output>
496 </test>
497
498 <!-- Test with GFF3 -->
499 <test>
500 <param name="genome_name" value="Dbia3"/>
501 <param name="fasta_file" value="common/dbia3.fa"/>
502 <repeat name="group">
503 <param name="group_name" value="Default group"/>
504 <repeat name="format">
505 <conditional name="formatChoice">
506 <param name="format_select" value="gff3"/>
507 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
508 <param name="track_color" value="#000000"/>
509 </conditional>
510 </repeat>
511 </repeat>
512 <output name="output" file="gff3/gff3_trackhub.html">
513 <!-- Verify tracks folder contains bam and bai -->
514 <extra_files type="file"
515 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
516 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
517 compare="sim_size"
518 />
519 <!-- Verify trackDb.txt contains the basic fields for a bam -->
520 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
521 </output>
522 </test>
523
524 <!-- Test with GTF -->
525 <test>
526 <param name="genome_name" value="Dbia3"/>
527 <param name="fasta_file" value="common/dbia3.fa"/>
528 <repeat name="group">
529 <param name="group_name" value="Default group"/>
530 <repeat name="format">
531 <conditional name="formatChoice">
532 <param name="format_select" value="gtf"/>
533 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
534 <param name="track_color" value="#000000"/>
535 </conditional>
536 </repeat>
537 </repeat>
538 <output name="output" file="gtf/gtf_trackhub.html">
539 <!-- Verify tracks folder contains bam and bai -->
540 <extra_files type="file"
541 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
542 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
543 compare="sim_size"
544 />
545 <!-- Verify trackDb.txt contains the basic fields for a bam -->
546 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
547 </output>
548 </test>
549
550 <!-- Test with one group and multiple tracks -->
551 <test>
552 <param name="genome_name" value="Dbia3"/>
553 <param name="fasta_file" value="common/dbia3.fa"/>
554 <repeat name="group">
555 <param name="group_name" value="Default group"/>
556 <repeat name="format">
557 <conditional name="formatChoice">
558 <param name="format_select" value="gtf"/>
559 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
560 <param name="track_color" value="#000000"/>
561 </conditional>
562 </repeat>
563 <repeat name="format">
564 <conditional name="formatChoice">
565 <param name="format_select" value="gff3"/>
566 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
567 <param name="track_color" value="#000000"/>
568 </conditional>
569 </repeat>
570 </repeat>
571 <output name="output" file="gtf_gff/gtf_gff_trackhub.html">
572 <!-- verify tracks folder contains bam and bai -->
573 <extra_files type="file"
574 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
575 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
576 compare="sim_size"
577 />
578 <extra_files type="file"
579 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
580 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
581 compare="sim_size"
582 />
583 <!-- verify trackdb.txt contains the basic fields for a bam -->
584 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
585 </output>
586 </test>
587
588 <!-- Test with one group and all the supported datatypes on 10/04/2016 -->
589 <test>
590 <param name="genome_name" value="Dbia3"/>
591 <param name="fasta_file" value="common/dbia3.fa"/>
592 <repeat name="group">
593 <param name="group_name" value="Default group"/>
594 <repeat name="format">
595 <conditional name="formatChoice">
596 <param name="format_select" value="bam"/>
597 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
598 <param name="track_color" value="#000000"/>
599 </conditional>
600 </repeat>
601 <repeat name="format">
602 <conditional name="formatChoice">
603 <param name="format_select" value="bed"/>
604 <conditional name="bedChoice">
605 <param name="bed_select" value="bed_generic"/>
606 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
607 <param name="track_color" value="#000000"/>
608 </conditional>
609 </conditional>
610 </repeat>
611 <repeat name="format">
612 <conditional name="formatChoice">
613 <param name="format_select" value="bed"/>
614 <conditional name="bedChoice">
615 <param name="bed_select" value="bed_simple_repeats_option"/>
616 <param name="BED_simple_repeats" ftype="bed"
617 value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
618 <param name="track_color" value="#000000"/>
619 </conditional>
620 </conditional>
621 </repeat>
622 <repeat name="format">
623 <conditional name="formatChoice">
624 <param name="format_select" value="psl"/>
625 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
626 <param name="track_color" value="#000000"/>
627 </conditional>
628 </repeat>
629 <repeat name="format">
630 <conditional name="formatChoice">
631 <param name="format_select" value="bigwig"/>
632 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
633 <param name="track_color" value="#000000"/>
634 </conditional>
635 </repeat>
636 <repeat name="format">
637 <conditional name="formatChoice">
638 <param name="format_select" value="gff3"/>
639 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
640 <param name="track_color" value="#000000"/>
641 </conditional>
642 </repeat>
643 <repeat name="format">
644 <conditional name="formatChoice">
645 <param name="format_select" value="gtf"/>
646 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
647 <param name="track_color" value="#000000"/>
648 </conditional>
649 </repeat>
650 </repeat>
651 <output name="output" file="all_datatypes/all_datatypes_trackhub.html">
652 <!-- verify tracks folder contains all the files -->
653 <extra_files type="file"
654 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
655 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
656 compare="sim_size"
657 />
658 <extra_files type="file"
659 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
660 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
661 compare="sim_size"
662 />
663 <extra_files type="file"
664 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
665 value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
666 compare="sim_size"
667 />
668 <extra_files type="file"
669 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
670 value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
671 compare="sim_size"
672 />
673 <extra_files type="file"
674 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
675 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb"
676 compare="sim_size"
677 />
678 <extra_files type="file"
679 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
680 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
681 compare="sim_size"
682 />
683 <extra_files type="file"
684 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
685 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
686 compare="sim_size"
687 />
688 <extra_files type="file"
689 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
690 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
691 compare="sim_size"
692 />
693 <!-- verify trackdb.txt contains the basic fields for a bam -->
694 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
695 </output>
696 </test>
697
698 <!-- Test with two groups and no tracks -->
699 <test>
700 <param name="genome_name" value="Dbia3"/>
701 <param name="fasta_file" value="common/dbia3.fa"/>
702 <repeat name="group">
703 <param name="group_name" value="Default group"/>
704 </repeat>
705 <repeat name="group">
706 <param name="group_name" value="Other group"/>
707 </repeat>
708 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
709 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_no_track/myHub/genomes.txt"/>
710 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_no_track/myHub/Dbia3.html"/>
711 <!-- Email could be different, but we need to ensure we still have the email line -->
712 <extra_files type="file" name="myHub/hub.txt" value="two_groups_no_track/myHub/hub.txt" lines_diff="2">
713 <assert_contents>
714 <has_text text="email"/>
715 </assert_contents>
716 </extra_files>
717 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
718 </extra_files>
719 <extra_files type="file" name="myHub/Dbia3/description.html"
720 value="two_groups_no_track/myHub/Dbia3/description.html"/>
721 </output>
722 </test>
723
724 <!-- Test with two groups and one track in first -->
725 <test>
726 <param name="genome_name" value="Dbia3"/>
727 <param name="fasta_file" value="common/dbia3.fa"/>
728 <repeat name="group">
729 <param name="group_name" value="Default group"/>
730 <repeat name="format">
731 <conditional name="formatChoice">
732 <param name="format_select" value="bigwig"/>
733 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
734 <param name="track_color" value="#000000"/>
735 </conditional>
736 </repeat>
737 </repeat>
738 <repeat name="group">
739 <param name="group_name" value="Other group"/>
740 </repeat>
741 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">
742 <!-- Check myHub structure -->
743 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_first/myHub/genomes.txt"/>
744 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_first/myHub/Dbia3.html"/>
745 <!-- Email could be different, but we need to ensure we still have the email line -->
746 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_first/myHub/hub.txt" lines_diff="2">
747 <assert_contents>
748 <has_text text="email"/>
749 </assert_contents>
750 </extra_files>
751 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
752 </extra_files>
753 <extra_files type="file" name="myHub/Dbia3/description.html"
754 value="two_groups_one_track_first/myHub/Dbia3/description.html"/>
755
756 <!-- Check tracks exist -->
757 <extra_files type="file"
758 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
759 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
760 compare="sim_size"
761 />
762
763 <!-- Check the groups.txt exists and is properly populated -->
764 </output>
765 </test>
766
767 <!-- Test with two groups and one track in both -->
768 <test>
769 <param name="genome_name" value="Dbia3"/>
770 <param name="fasta_file" value="common/dbia3.fa"/>
771 <repeat name="group">
772 <param name="group_name" value="Default group"/>
773 <repeat name="format">
774 <conditional name="formatChoice">
775 <param name="format_select" value="bigwig"/>
776 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
777 <param name="track_color" value="#000000"/>
778 </conditional>
779 </repeat>
780 </repeat>
781 <repeat name="group">
782 <param name="group_name" value="Other group"/>
783 <repeat name="format">
784 <conditional name="formatChoice">
785 <param name="format_select" value="gtf"/>
786 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
787 <param name="track_color" value="#000000"/>
788 </conditional>
789 </repeat>
790 </repeat>
791 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">
792 <!-- Check myHub structure -->
793 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_both/myHub/genomes.txt"/>
794 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_both/myHub/Dbia3.html"/>
795 <!-- Email could be different, but we need to ensure we still have the email line -->
796 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_both/myHub/hub.txt"
797 lines_diff="2">
798 <assert_contents>
799 <has_text text="email"/>
800 </assert_contents>
801 </extra_files>
802 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
803 </extra_files>
804 <extra_files type="file" name="myHub/Dbia3/description.html"
805 value="two_groups_one_track_both/myHub/Dbia3/description.html"/>
806
807 <!-- Check tracks exist -->
808 <!-- First group -->
809 <extra_files type="file"
810 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
811 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
812 compare="sim_size"
813 />
814
815 <!-- Second group -->
816 <extra_files type="file"
817 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
818 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
819 compare="sim_size"
820 />
821 <!-- Check the groups.txt exists and is properly populated -->
822 </output>
823 </test>
824
825 <!-- Test with two groups and multiple tracks in both -->
826 <test>
827 <param name="genome_name" value="Dbia3"/>
828 <param name="fasta_file" value="common/dbia3.fa"/>
829 <repeat name="group">
830 <param name="group_name" value="Default group"/>
831 <repeat name="format">
832 <conditional name="formatChoice">
833 <param name="format_select" value="bigwig"/>
834 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
835 <param name="track_color" value="#000000"/>
836 </conditional>
837 </repeat>
838 <repeat name="format">
839 <conditional name="formatChoice">
840 <param name="format_select" value="bam"/>
841 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
842 <param name="track_color" value="#000000"/>
843 </conditional>
844 </repeat>
845 </repeat>
846 <repeat name="group">
847 <param name="group_name" value="Other group"/>
848 <repeat name="format">
849 <conditional name="formatChoice">
850 <param name="format_select" value="gtf"/>
851 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
852 <param name="track_color" value="#000000"/>
853 </conditional>
854 </repeat>
855 <repeat name="format">
856 <conditional name="formatChoice">
857 <param name="format_select" value="gff3"/>
858 <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/>
859 <param name="track_color" value="#000000"/>
860 </conditional>
861 </repeat>
862 </repeat>
863 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">
864 <!-- Check myHub structure -->
865 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_multiple_tracks/myHub/genomes.txt"/>
866 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_multiple_tracks/myHub/Dbia3.html"/>
867 <!-- Email could be different, but we need to ensure we still have the email line -->
868 <extra_files type="file" name="myHub/hub.txt" value="two_groups_multiple_tracks/myHub/hub.txt"
869 lines_diff="2">
870 <assert_contents>
871 <has_text text="email"/>
872 </assert_contents>
873 </extra_files>
874 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
875 </extra_files>
876 <extra_files type="file" name="myHub/Dbia3/description.html"
877 value="two_groups_multiple_tracks/myHub/Dbia3/description.html"/>
878
879 <!-- Check tracks exist -->
880 <!-- First group -->
881 <extra_files type="file"
882 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
883 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
884 compare="sim_size"
885 />
886 <extra_files type="file"
887 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
888 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
889 compare="sim_size"
890 />
891 <extra_files type="file"
892 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
893 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
894 compare="sim_size"
895 />
896
897 <!-- Second group -->
898 <extra_files type="file"
899 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
900 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
901 compare="sim_size"
902 />
903 <extra_files type="file"
904 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
905 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
906 compare="sim_size"
907 />
908 <!-- Check the groups.txt exists and is properly populated -->
909 </output>
910 </test>
911
912 <!-- Test default color in a track -->
913 <test>
914 <param name="genome_name" value="Dbia3"/>
915 <param name="fasta_file" value="common/dbia3.fa"/>
916 <repeat name="group">
917 <param name="group_name" value="Default group"/>
918 <repeat name="format">
919 <conditional name="formatChoice">
920 <param name="format_select" value="bam"/>
921 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
922 <param name="track_color" value="#000000"/>
923 </conditional>
924 </repeat>
925 </repeat>
926 <output name="output" file="default_color/default_color_trackhub.html">
927 <!-- Verify trackDb.txt contains the color 0,0,0 -->
928 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="default_color/myHub/Dbia3/trackDb.txt">
929 <assert_contents>
930 <has_text text="color 0,0,0"/>
931 </assert_contents>
932 </extra_files>
933
934 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
935 </output>
936 </test>
937
938 <!-- Test changed color in a track -->
939 <test>
940 <param name="genome_name" value="Dbia3"/>
941 <param name="fasta_file" value="common/dbia3.fa"/>
942 <repeat name="group">
943 <param name="group_name" value="Default group"/>
944 <repeat name="format">
945 <conditional name="formatChoice">
946 <param name="format_select" value="bam"/>
947 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
948 <param name="track_color" value="#8064a2"/>
949 </conditional>
950 </repeat>
951 </repeat>
952 <output name="output" file="changed_color/changed_color_trackhub.html">
953 <!-- Verify trackDb.txt contains the color 128,100,162 -->
954 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="changed_color/myHub/Dbia3/trackDb.txt">
955 <assert_contents>
956 <has_text text="color 128,100,162"/>
957 </assert_contents>
958 </extra_files>
959
960 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
961 </output>
962 </test>
963
964 <!-- Test for StringTie Chromosome end coordinates -->
965 <test>
966 <param name="genome_name" value="Dbia3"/>
967 <param name="fasta_file" value="common/dbia3.fa"/>
968 <repeat name="group">
969 <param name="group_name" value="Default group"/>
970 <repeat name="format">
971 <conditional name="formatChoice">
972 <param name="format_select" value="gtf"/>
973 <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>
974 <param name="track_color" value="#000000"/>
975 </conditional>
976 </repeat>
977 </repeat>
978 <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">
979 <extra_files type="file"
980 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
981 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
982 compare="sim_size"
983 />
984
985 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
986 </output>
987 </test>
988
989 <!-- Test for big files? -->
990
991 <!-- Find tests that should fail -->
992
993 </tests>
994
995 <help>
996 This Galaxy tool permits to prepare your files to be ready for
997 Assembly Hub visualization.
998 </help>
999 </tool>