Mercurial > repos > rmarenco > hubarchivecreator

comparison tests.xml @ 29:7e8a8b732db3 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
author yating-l
date Wed, 16 May 2018 18:04:20 -0400
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28:6aa28a85cc38 29:7e8a8b732db3
1 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
2 #set database = str($f.formatChoice.bedChoice.database)
3 #silent $extra_data_dict.update({"database": $database})
4 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
5 #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index
6 #if $i.element_identifier.endswith("ix")
7 #$extra_data_dict.update({"index_ix": str($i)})
8 #elif $i.element_identifier.endswith("ixx")
9 #$extra_data_dict.update({"index_ixx": str($i)})
10 #end if
11 #end for
12 ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix)
13 ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx)
14 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
15 #end if
16 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
17 $extra_data_dict)
18 #end if
19 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
20 #set database = str($f.formatChoice.bedChoice.database)
21 #silent $extra_data_dict.update({"database": $database})
22 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
23 #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index
24 #if $i.element_identifier.endswith("ix")
25 #$extra_data_dict.update({"index_ix": str($i)})
26 #elif $i.element_identifier.endswith("ixx")
27 #$extra_data_dict.update({"index_ixx": str($i)})
28 #end if
29 #end for
30 ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix)
31 ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx)
32 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
33 #end if
34 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
35 $extra_data_dict)
36 #end if
37
38 #if $f.formatChoice.format_select == "bigbed"
39 #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes"
40 ##set ix_index = str($f.formatChoice.add_trix_index.trix_index.index_ix)
41 ##set ixx_index = str($f.formatChoice.add_trix_index.trix_index.index_ixx)
42 #for i in $f.formatChoice.add_trix_index.trix_index
43 #if $i.element_identifier.endswith("ix")
44 #$extra_data_dict.update({"index_ix": str($i)})
45 #elif $i.element_identifier.endswith("ixx")
46 #$extra_data_dict.update({"index_ixx": str($i)})
47 #end if
48 #end for
49 #$extra_data_dict.update({"trix_id": str($f.formatChoice.add_trix_index.trix_id)})
50 ##set trix_id = str($f.formatChoice.add_trix_index.trix_id)
51 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id})
52 #end if
53 #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final,
54 $extra_data_dict)
55 #end if
56 <!-- Test with only the fasta file -->
57 <test>
58 <param name="genome_name" value="Dbia3"/>
59 <param name="fasta_file" value="common/dbia3.fa"/>
60 <output name="output" file="only_genome/only_genome.html">
61 <!-- Use macro to check the whole common structure without repeated code -->
62 <expand macro="verify_hub_structure_no_track" test="only_genome" />
63 </output>
64 </test>
65
66 <!-- Test with Bam -->
67 <test>
68 <param name="genome_name" value="Dbia3"/>
69 <param name="fasta_file" value="common/dbia3.fa"/>
70 <repeat name="group">
71 <param name="group_name" value="Default group"/>
72 <repeat name="format">
73 <conditional name="formatChoice">
74 <param name="format_select" value="bam"/>
75 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
76 <param name="longLabel" value="HISAT sequence alignment" />
77 <param name="track_color" value="#000000"/>
78 </conditional>
79 </repeat>
80 </repeat>
81 <output name="output" file="bam/bam.html">
82 <!-- Verify tracks folder contains bam and bai -->
83 <extra_files type="file"
84 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
85 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
86 compare="sim_size"
87 />
88 <extra_files type="file"
89 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
90 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
91 compare="sim_size"
92 />
93 <!-- Use macro to check the whole common structure without repeated code -->
94 <expand macro="verify_hub_structure" test="bam" />
95 </output>
96 </test>
97
98 <!-- Test with Bed Generic -->
99 <test>
100 <param name="genome_name" value="Dbia3"/>
101 <param name="fasta_file" value="common/dbia3.fa"/>
102 <repeat name="group">
103 <param name="group_name" value="Default group"/>
104 <repeat name="format">
105 <conditional name="formatChoice">
106 <param name="format_select" value="bed" />
107 <conditional name="bedChoice">
108 <param name="bed_select" value="bed_generic"/>
109 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
110 <param name="longLabel" value="TBLASTN alignment" />
111 <param name="track_color" value="#000000"/>
112 </conditional>
113 </conditional>
114 </repeat>
115 </repeat>
116 <output name="output" file="bed_generic/bed_generic.html">
117 <extra_files type="file"
118 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
119 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
120 compare="sim_size"
121 />
122 <expand macro="verify_hub_structure" test="bed_generic" />
123 </output>
124 </test>
125
126 <!-- Test with Bed Simple repeat -->
127 <test>
128 <param name="genome_name" value="Dbia3"/>
129 <param name="fasta_file" value="common/dbia3.fa"/>
130 <repeat name="group">
131 <param name="group_name" value="Default group"/>
132 <repeat name="format">
133 <conditional name="formatChoice">
134 <param name="format_select" value="bed" />
135 <conditional name="bedChoice">
136 <param name="bed_select" value="bed_simple_repeats_option"/>
137 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
138 <param name="longLabel" value="Simple repeat" />
139 <param name="track_color" value="#000000"/>
140 </conditional>
141 </conditional>
142 </repeat>
143 </repeat>
144 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
145 <extra_files type="file"
146 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
147 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
148 compare="sim_size"
149 />
150 <expand macro="verify_hub_structure" test="bed_simple_repeats" />
151 </output>
152 </test>
153
154 <!-- Test with Psl -->
155 <test>
156 <param name="genome_name" value="Dbia3"/>
157 <param name="fasta_file" value="common/dbia3.fa"/>
158 <repeat name="group">
159 <param name="group_name" value="Default group"/>
160 <repeat name="format">
161 <conditional name="formatChoice">
162 <param name="format_select" value="psl"/>
163 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
164 <param name="longLabel" value="BLAST Alignment" />
165 <param name="track_color" value="#000000"/>
166 </conditional>
167 </repeat>
168 </repeat>
169 <output name="output" file="psl/psl_trackhub.html">
170 <extra_files type="file"
171 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
172 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
173 compare="sim_size"
174 />
175 <expand macro="verify_hub_structure" test="psl" />
176 </output>
177 </test>
178
179 <!-- Test with BigWig -->
180 <test>
181 <param name="genome_name" value="Dbia3"/>
182 <param name="fasta_file" value="common/dbia3.fa"/>
183 <repeat name="group">
184 <param name="group_name" value="Default group"/>
185 <repeat name="format">
186 <conditional name="formatChoice">
187 <param name="format_select" value="bigwig"/>
188 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
189 <param name="longLabel" value="RNA-Seq Coverage" />
190 <param name="track_color" value="#000000"/>
191 </conditional>
192 </repeat>
193 </repeat>
194 <output name="output" file="bigwig/bigwig.html">
195 <extra_files type="file"
196 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
197 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
198 compare="sim_size"
199 />
200 <expand macro="verify_hub_structure" test="bigwig" />
201 <!-- check additional trackDb settings for BigWig -->
202 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
203 <assert_contents>
204 <has_text text="autoScale"/>
205 <has_text text="maxHeightPixels"/>
206 <has_text text="windowingFunction"/>
207 </assert_contents>
208 </extra_files>
209 </output>
210 </test>
211
212 <!-- Test with GFF3 -->
213 <test>
214 <param name="genome_name" value="Dbia3"/>
215 <param name="fasta_file" value="common/dbia3.fa"/>
216 <repeat name="group">
217 <param name="group_name" value="Default group"/>
218 <repeat name="format">
219 <conditional name="formatChoice">
220 <param name="format_select" value="gff3"/>
221 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
222 <param name="longLabel" value="Augustus" />
223 <param name="track_color" value="#000000"/>
224 </conditional>
225 </repeat>
226 </repeat>
227 <output name="output" file="gff3/gff3_trackhub.html">
228 <extra_files type="file"
229 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
230 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
231 compare="sim_size"
232 />
233 <expand macro="verify_hub_structure" test="gff3" />
234 </output>
235 </test>
236
237 <!-- Test with GTF -->
238 <test>
239 <param name="genome_name" value="Dbia3"/>
240 <param name="fasta_file" value="common/dbia3.fa"/>
241 <repeat name="group">
242 <param name="group_name" value="Default group"/>
243 <repeat name="format">
244 <conditional name="formatChoice">
245 <param name="format_select" value="gtf"/>
246 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
247 <param name="longLabel" value="StringTie transcripts" />
248 <param name="track_color" value="#000000"/>
249 </conditional>
250 </repeat>
251 </repeat>
252 <output name="output" file="gtf/gtf_trackhub.html">
253 <extra_files type="file"
254 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
255 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
256 compare="sim_size"
257 />
258 <expand macro="verify_hub_structure" test="gtf" />
259 </output>
260 </test>
261
262 <!-- Test with BLAT Alignment -->
263 <test>
264 <param name="genome_name" value="Dbia3"/>
265 <param name="fasta_file" value="common/dbia3.fa"/>
266 <repeat name="group">
267 <param name="group_name" value="Default group"/>
268 <repeat name="format">
269 <conditional name="formatChoice">
270 <param name="format_select" value="bed" />
271 <conditional name="bedChoice">
272 <param name="bed_select" value="bed_blat_alignment_option"/>
273 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
274 <param name="longLabel" value="BLAT alignment" />
275 <param name="track_color" value="#000000"/>
276 <param name="database" value="NCBI" />
277 </conditional>
278 </conditional>
279 </repeat>
280 </repeat>
281 <output name="output" file="bed_blat_alignment/blat_alignment_trackhub.html">
282 <extra_files type="file"
283 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
284 value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
285 compare="sim_size"
286 />
287 <expand macro="verify_hub_structure" test="bed_blat_alignment" />
288 <!-- check additional trackDb settings for BLAT -->
289 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
290 <assert_contents>
291 <has_text text="searchIndex"/>
292 <has_text text="url"/>
293 <has_text text="urlLabel"/>
294 <has_text text="iframeUrl"/>
295 <has_text text="iframeOptions"/>
296 </assert_contents>
297 </extra_files>
298 </output>
299 </test>
300
301 <!-- Test with BLAST Alignment -->
302 <test>
303 <param name="genome_name" value="Dbia3"/>
304 <param name="fasta_file" value="common/dbia3.fa"/>
305 <repeat name="group">
306 <param name="group_name" value="Default group"/>
307 <repeat name="format">
308 <conditional name="formatChoice">
309 <param name="format_select" value="bed" />
310 <conditional name="bedChoice">
311 <param name="bed_select" value="bed_blast_alignment_option"/>
312 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
313 <param name="longLabel" value="BLAST alignment" />
314 <param name="track_color" value="#000000"/>
315 <param name="database" value="NCBI" />
316 </conditional>
317 </conditional>
318 </repeat>
319 </repeat>
320 <output name="output" file="bed_blast_alignment/blast_alignment_trackhub.html">
321 <extra_files type="file"
322 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
323 value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
324 compare="sim_size"
325 />
326 <expand macro="verify_hub_structure" test="bed_blast_alignment" />
327 <!-- check additional trackDb settings for BLAST -->
328 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
329 <assert_contents>
330 <has_text text="searchIndex"/>
331 <has_text text="url"/>
332 <has_text text="urlLabel"/>
333 <has_text text="iframeUrl"/>
334 <has_text text="iframeOptions"/>
335 </assert_contents>
336 </extra_files>
337 </output>
338 </test>
339
340 <!-- Test with Regtools Splice Junctions -->
341 <test>
342 <param name="genome_name" value="Dbia3"/>
343 <param name="fasta_file" value="common/dbia3.fa"/>
344 <repeat name="group">
345 <param name="group_name" value="Default group"/>
346 <repeat name="format">
347 <conditional name="formatChoice">
348 <param name="format_select" value="bed" />
349 <conditional name="bedChoice">
350 <param name="bed_select" value="bed_splice_junctions_option"/>
351 <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/>
352 <param name="longLabel" value="Splice junctions" />
353 <param name="track_color" value="#000000"/>
354 </conditional>
355 </conditional>
356 </repeat>
357 </repeat>
358 <output name="output" file="bed_splice_junctions/splice_junctions_trackhub.html">
359 <extra_files type="file"
360 name="myHub/Dbia3/tracks/regtools_junctions.bb"
361 value="bed_splice_junctions/myHub/Dbia3/tracks/regtools_junctions.bb"
362 compare="sim_size"
363 />
364 <expand macro="verify_hub_structure" test="bed_splice_junctions" />
365 </output>
366 </test>
367
368 <!-- Test with Cytoband -->
369 <test>
370 <param name="genome_name" value="Dbia3"/>
371 <param name="fasta_file" value="common/dbia3.fa"/>
372 <repeat name="group">
373 <param name="group_name" value="Default group"/>
374 <repeat name="format">
375 <conditional name="formatChoice">
376 <param name="format_select" value="bed" />
377 <conditional name="bedChoice">
378 <param name="bed_select" value="bed_cytoBand"/>
379 <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/>
380 <param name="longLabel" value="Cytoband" />
381 <param name="track_color" value="#000000"/>
382 </conditional>
383 </conditional>
384 </repeat>
385 </repeat>
386 <output name="output" file="bed_cytoband/cytoband_trackhub.html">
387 <extra_files type="file"
388 name="myHub/Dbia3/tracks/Cytoband.bb"
389 value="bed_cytoband/myHub/Dbia3/tracks/Cytoband.bb"
390 compare="sim_size"
391 />
392 <expand macro="verify_hub_structure" test="bed_cytoband" />
393 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
394 <assert_contents>
395 <has_text text="track cytoBandIdeo"/>
396 </assert_contents>
397 </extra_files>
398 </output>
399 </test>
400
401 <!-- Test with bigBed -->
402 <test>
403 <param name="genome_name" value="Dbia3"/>
404 <param name="fasta_file" value="common/dbia3.fa"/>
405 <repeat name="group">
406 <param name="group_name" value="Default group"/>
407 <repeat name="format">
408 <conditional name="formatChoice">
409 <param name="format_select" value="bigbed"/>
410 <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />
411 <param name="longLabel" value="bigBed" />
412 <param name="track_color" value="#000000"/>
413 </conditional>
414 </repeat>
415 </repeat>
416 <output name="output" file="big_bed/bigbed_trackhub.html">
417 <extra_files type="file"
418 name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
419 value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
420 compare="sim_size"
421 />
422 <expand macro="verify_hub_structure" test="big_bed" />
423 </output>
424 </test>
425
426 <!-- Test with one group and multiple tracks -->
427 <test>
428 <param name="genome_name" value="Dbia3"/>
429 <param name="fasta_file" value="common/dbia3.fa"/>
430 <repeat name="group">
431 <param name="group_name" value="Default group"/>
432 <repeat name="format">
433 <conditional name="formatChoice">
434 <param name="format_select" value="gtf"/>
435 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
436 <param name="track_color" value="#000000"/>
437 </conditional>
438 </repeat>
439 <repeat name="format">
440 <conditional name="formatChoice">
441 <param name="format_select" value="gff3"/>
442 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
443 <param name="track_color" value="#000000"/>
444 </conditional>
445 </repeat>
446 </repeat>
447 <output name="output" file="gtf_gff/gtf_gff_trackhub.html">
448 <extra_files type="file"
449 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
450 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
451 compare="sim_size"
452 />
453 <extra_files type="file"
454 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
455 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
456 compare="sim_size"
457 />
458 <expand macro="verify_hub_structure" test="gtf_gff" />
459 </output>
460 </test>
461
462 <!-- Test with one group and all the supported datatypes -->
463 <test>
464 <param name="genome_name" value="Dbia3"/>
465 <param name="fasta_file" value="common/dbia3.fa"/>
466 <repeat name="group">
467 <param name="group_name" value="Default group"/>
468 <repeat name="format">
469 <conditional name="formatChoice">
470 <param name="format_select" value="bam"/>
471 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
472 <param name="track_color" value="#000000"/>
473 </conditional>
474 </repeat>
475 <repeat name="format">
476 <conditional name="formatChoice">
477 <param name="format_select" value="bed"/>
478 <conditional name="bedChoice">
479 <param name="bed_select" value="bed_generic"/>
480 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
481 <param name="track_color" value="#000000"/>
482 </conditional>
483 </conditional>
484 </repeat>
485 <repeat name="format">
486 <conditional name="formatChoice">
487 <param name="format_select" value="bed"/>
488 <conditional name="bedChoice">
489 <param name="bed_select" value="bed_simple_repeats_option"/>
490 <param name="BED_simple_repeats" ftype="bed"
491 value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
492 <param name="track_color" value="#000000"/>
493 </conditional>
494 </conditional>
495 </repeat>
496 <repeat name="format">
497 <conditional name="formatChoice">
498 <param name="format_select" value="psl"/>
499 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
500 <param name="track_color" value="#000000"/>
501 </conditional>
502 </repeat>
503 <repeat name="format">
504 <conditional name="formatChoice">
505 <param name="format_select" value="bigwig"/>
506 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
507 <param name="track_color" value="#000000"/>
508 </conditional>
509 </repeat>
510 <repeat name="format">
511 <conditional name="formatChoice">
512 <param name="format_select" value="gff3"/>
513 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
514 <param name="track_color" value="#000000"/>
515 </conditional>
516 </repeat>
517 <repeat name="format">
518 <conditional name="formatChoice">
519 <param name="format_select" value="gtf"/>
520 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
521 <param name="track_color" value="#000000"/>
522 </conditional>
523 </repeat>
524 <repeat name="format">
525 <conditional name="formatChoice">
526 <param name="format_select" value="bed" />
527 <conditional name="bedChoice">
528 <param name="bed_select" value="bed_cytoBand"/>
529 <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/>
530 <param name="track_color" value="#000000"/>
531 </conditional>
532 </conditional>
533 </repeat>
534 <repeat name="format">
535 <conditional name="formatChoice">
536 <param name="format_select" value="bed" />
537 <conditional name="bedChoice">
538 <param name="bed_select" value="bed_splice_junctions_option"/>
539 <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/>
540 <param name="track_color" value="#000000"/>
541 </conditional>
542 </conditional>
543 </repeat>
544 <repeat name="format">
545 <conditional name="formatChoice">
546 <param name="format_select" value="bed" />
547 <conditional name="bedChoice">
548 <param name="bed_select" value="bed_blast_alignment_option"/>
549 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
550 <param name="track_color" value="#000000"/>
551 <param name="database" value="NCBI" />
552 </conditional>
553 </conditional>
554 </repeat>
555 <repeat name="format">
556 <conditional name="formatChoice">
557 <param name="format_select" value="bed" />
558 <conditional name="bedChoice">
559 <param name="bed_select" value="bed_blat_alignment_option"/>
560 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
561 <param name="track_color" value="#000000"/>
562 <param name="database" value="NCBI" />
563 </conditional>
564 </conditional>
565 </repeat>
566 </repeat>
567 <output name="output" file="all_datatypes/all_datatypes_trackhub.html">
568 <!-- verify tracks folder contains all the files -->
569 <extra_files type="file"
570 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
571 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
572 compare="sim_size"
573 />
574 <extra_files type="file"
575 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
576 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
577 compare="sim_size"
578 />
579 <extra_files type="file"
580 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
581 value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
582 compare="sim_size"
583 />
584 <extra_files type="file"
585 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
586 value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
587 compare="sim_size"
588 />
589 <extra_files type="file"
590 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
591 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb"
592 compare="sim_size"
593 />
594 <extra_files type="file"
595 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
596 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
597 compare="sim_size"
598 />
599 <extra_files type="file"
600 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
601 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
602 compare="sim_size"
603 />
604 <extra_files type="file"
605 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
606 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
607 compare="sim_size"
608 />
609 <extra_files type="file"
610 name="myHub/Dbia3/tracks/Cytoband.bb"
611 value="all_datatypes/myHub/Dbia3/tracks/Cytoband.bb"
612 compare="sim_size"
613 />
614 <extra_files type="file"
615 name="myHub/Dbia3/tracks/regtools_junctions.bb"
616 value="all_datatypes/myHub/Dbia3/tracks/regtools_junctions.bb"
617 compare="sim_size"
618 />
619 <extra_files type="file"
620 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
621 value="all_datatypes/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
622 compare="sim_size"
623 />
624 <extra_files type="file"
625 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
626 value="all_datatypes/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
627 compare="sim_size"
628 />
629 <expand macro="verify_hub_structure" test="all_datatypes" />
630 </output>
631 </test>
632
633 <!-- Test with two groups and no tracks -->
634 <test>
635 <param name="genome_name" value="Dbia3"/>
636 <param name="fasta_file" value="common/dbia3.fa"/>
637 <repeat name="group">
638 <param name="group_name" value="Default group"/>
639 </repeat>
640 <repeat name="group">
641 <param name="group_name" value="Other group"/>
642 </repeat>
643 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
644 <expand macro="verify_hub_structure_no_track" test="two_groups_no_track" />
645 </output>
646 </test>
647
648 <!-- Test with two groups and one track in first -->
649 <test>
650 <param name="genome_name" value="Dbia3"/>
651 <param name="fasta_file" value="common/dbia3.fa"/>
652 <repeat name="group">
653 <param name="group_name" value="Default group"/>
654 <repeat name="format">
655 <conditional name="formatChoice">
656 <param name="format_select" value="bigwig"/>
657 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
658 <param name="track_color" value="#000000"/>
659 </conditional>
660 </repeat>
661 </repeat>
662 <repeat name="group">
663 <param name="group_name" value="Other group"/>
664 </repeat>
665 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">
666 <!-- Check tracks exist -->
667 <extra_files type="file"
668 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
669 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
670 compare="sim_size"
671 />
672 <expand macro="verify_hub_structure" test="two_groups_one_track_first" />
673 </output>
674 </test>
675
676 <!-- Test with two groups and one track in both -->
677 <test>
678 <param name="genome_name" value="Dbia3"/>
679 <param name="fasta_file" value="common/dbia3.fa"/>
680 <repeat name="group">
681 <param name="group_name" value="Default group"/>
682 <repeat name="format">
683 <conditional name="formatChoice">
684 <param name="format_select" value="bigwig"/>
685 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
686 <param name="track_color" value="#000000"/>
687 </conditional>
688 </repeat>
689 </repeat>
690 <repeat name="group">
691 <param name="group_name" value="Other group"/>
692 <repeat name="format">
693 <conditional name="formatChoice">
694 <param name="format_select" value="gtf"/>
695 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
696 <param name="track_color" value="#000000"/>
697 </conditional>
698 </repeat>
699 </repeat>
700 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">
701 <!-- Check tracks exist -->
702 <!-- First group -->
703 <extra_files type="file"
704 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
705 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
706 compare="sim_size"
707 />
708
709 <!-- Second group -->
710 <extra_files type="file"
711 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
712 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
713 compare="sim_size"
714 />
715 <expand macro="verify_hub_structure" test="two_groups_one_track_both" />
716 <!-- Check the groups.txt exists and is properly populated -->
717 </output>
718 </test>
719
720 <!-- Test with two groups and multiple tracks in both -->
721 <test>
722 <param name="genome_name" value="Dbia3"/>
723 <param name="fasta_file" value="common/dbia3.fa"/>
724 <repeat name="group">
725 <param name="group_name" value="Default group"/>
726 <repeat name="format">
727 <conditional name="formatChoice">
728 <param name="format_select" value="bigwig"/>
729 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
730 <param name="track_color" value="#000000"/>
731 </conditional>
732 </repeat>
733 <repeat name="format">
734 <conditional name="formatChoice">
735 <param name="format_select" value="bam"/>
736 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
737 <param name="track_color" value="#000000"/>
738 </conditional>
739 </repeat>
740 </repeat>
741 <repeat name="group">
742 <param name="group_name" value="Other group"/>
743 <repeat name="format">
744 <conditional name="formatChoice">
745 <param name="format_select" value="gtf"/>
746 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
747 <param name="track_color" value="#000000"/>
748 </conditional>
749 </repeat>
750 <repeat name="format">
751 <conditional name="formatChoice">
752 <param name="format_select" value="gff3"/>
753 <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/>
754 <param name="track_color" value="#000000"/>
755 </conditional>
756 </repeat>
757 </repeat>
758 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">
759 <!-- Check tracks exist -->
760 <!-- First group -->
761 <extra_files type="file"
762 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
763 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
764 compare="sim_size"
765 />
766 <extra_files type="file"
767 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
768 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
769 compare="sim_size"
770 />
771 <extra_files type="file"
772 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
773 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
774 compare="sim_size"
775 />
776
777 <!-- Second group -->
778 <extra_files type="file"
779 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
780 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
781 compare="sim_size"
782 />
783 <extra_files type="file"
784 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
785 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
786 compare="sim_size"
787 />
788 <expand macro="verify_hub_structure" test="two_groups_multiple_tracks" />
789 </output>
790 </test>
791
792 <!-- Test default color in a track -->
793 <test>
794 <param name="genome_name" value="Dbia3"/>
795 <param name="fasta_file" value="common/dbia3.fa"/>
796 <repeat name="group">
797 <param name="group_name" value="Default group"/>
798 <repeat name="format">
799 <conditional name="formatChoice">
800 <param name="format_select" value="bam"/>
801 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
802 <param name="track_color" value="#000000"/>
803 </conditional>
804 </repeat>
805 </repeat>
806 <output name="output" file="default_color/default_color_trackhub.html">
807 <expand macro="verify_hub_structure" test="default_color" />
808 <!-- Verify trackDb.txt contains the color 0,0,0 -->
809 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
810 <assert_contents>
811 <has_text text="color 0,0,0"/>
812 </assert_contents>
813 </extra_files>
814
815 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
816 </output>
817 </test>
818
819 <!-- Test changed color in a track -->
820 <test>
821 <param name="genome_name" value="Dbia3"/>
822 <param name="fasta_file" value="common/dbia3.fa"/>
823 <repeat name="group">
824 <param name="group_name" value="Default group"/>
825 <repeat name="format">
826 <conditional name="formatChoice">
827 <param name="format_select" value="bam"/>
828 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
829 <param name="track_color" value="#8064a2"/>
830 </conditional>
831 </repeat>
832 </repeat>
833 <output name="output" file="changed_color/changed_color_trackhub.html">
834 <expand macro="verify_hub_structure" test="changed_color" />
835 <!-- Verify trackDb.txt contains the color 128,100,162 -->
836 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
837 <assert_contents>
838 <has_text text="color 128,100,162"/>
839 </assert_contents>
840 </extra_files>
841
842 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
843 </output>
844 </test>
845
846 <!-- Test for StringTie Chromosome end coordinates -->
847 <test>
848 <param name="genome_name" value="Dbia3"/>
849 <param name="fasta_file" value="common/dbia3.fa"/>
850 <repeat name="group">
851 <param name="group_name" value="Default group"/>
852 <repeat name="format">
853 <conditional name="formatChoice">
854 <param name="format_select" value="gtf"/>
855 <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>
856 <param name="track_color" value="#000000"/>
857 </conditional>
858 </repeat>
859 </repeat>
860 <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">
861 <extra_files type="file"
862 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
863 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
864 compare="sim_size"
865 />
866 <expand macro="verify_hub_structure" test="stringtie_chromosome_end_coordinates" />
867
868 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
869 </output>
870 </test>
871
872 <!-- Test default label in a track -->
873 <test>
874 <param name="genome_name" value="Dbia3"/>
875 <param name="fasta_file" value="common/dbia3.fa"/>
876 <repeat name="group">
877 <param name="group_name" value="Default group"/>
878 <repeat name="format">
879 <conditional name="formatChoice">
880 <param name="format_select" value="bam"/>
881 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
882 <param name="track_color" value="#000000"/>
883 </conditional>
884 </repeat>
885 </repeat>
886 <output name="output" file="default_color/default_color_trackhub.html">
887 <expand macro="verify_hub_structure" test="default_color" />
888 <!-- Verify trackDb.txt contains default label -->
889 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
890 <assert_contents>
891 <has_text text="longLabel HISAT2 Accepted Hits.bam"/>
892 </assert_contents>
893 </extra_files>
894
895 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
896 </output>
897 </test>
898
899 <!-- Test customized label in a track -->
900 <test>
901 <param name="genome_name" value="Dbia3"/>
902 <param name="fasta_file" value="common/dbia3.fa"/>
903 <repeat name="group">
904 <param name="group_name" value="Default group"/>
905 <repeat name="format">
906 <conditional name="formatChoice">
907 <param name="format_select" value="bam"/>
908 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
909 <param name="longLabel" value="HISAT sequence alignment" />
910 <param name="track_color" value="#000000"/>
911 </conditional>
912 </repeat>
913 </repeat>
914 <output name="output" file="changed_label/changed_label_trackhub.html">
915 <expand macro="verify_hub_structure" test="changed_label" />
916 <!-- Verify trackDb.txt contains the customized label -->
917 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
918 <assert_contents>
919 <has_text text="longLabel HISAT sequence alignment"/>
920 </assert_contents>
921 </extra_files>
922
923 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
924 </output>
925 </test>