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comparison spades.xml @ 26:b512435320e3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
author iuc
date Wed, 12 Mar 2025 21:46:56 +0000
parents d5887ace0dd4
children
comparison
equal deleted inserted replaced
25:65d1598a9256 26:b512435320e3
45 @PIPELINE_OPTIONS@ 45 @PIPELINE_OPTIONS@
46 @PHREDOFFSET@ 46 @PHREDOFFSET@
47 47
48 ## postprocessing 48 ## postprocessing
49 @STATS@ 49 @STATS@
50 @CORRECTED@
51 ]]></command> 50 ]]></command>
52 <inputs> 51 <inputs>
53 <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/> 52 <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/>
54 <expand macro="input_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)"/> 53 <expand macro="input_files_all" format="@INTYPES@" label="FASTA/FASTQ file(s)"/>
55 <expand macro="input_additional_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)"/> 54 <expand macro="input_additional_files_all" format="@INTYPES@" label="FASTA/FASTQ file(s)"/>
56 <section name="arf" title="Additional read files"> 55 <section name="arf" title="Additional read files">
57 <expand macro="nanopore_pacbio"/> 56 <expand macro="nanopore_pacbio"/>
58 <expand macro="sanger"/> 57 <expand macro="sanger"/>
59 <expand macro="contigs"/> 58 <expand macro="contigs"/>
60 </section> 59 </section>
61 <expand macro="pipeline_options"> 60 <expand macro="pipeline_options" additional_help="&quot;Isolate&quot; is not compatible with &quot;Careful&quot; and Operation mode &quot;Only error correction&quot;">
62 <option value="--sc">Single cell mode: required for MDA (single-cell) data (--sc)</option> 61 <option value="--sc">Single cell mode: required for MDA (single-cell) data (--sc)</option>
63 <option value="--isolate">Isolate: highly recommended for high-coverage isolate and multi-cell data (--isolate)</option> 62 <option value="--isolate">Isolate: highly recommended for high-coverage isolate and multi-cell data (--isolate)</option>
64 <option value="--careful">Careful: ties to reduce the number of mismatches and short indels. Only recommended for small genomes (--careful)</option> 63 <option value="--careful">Careful: ties to reduce the number of mismatches and short indels. Only recommended for small genomes (--careful)</option>
65 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option> 64 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>
66 </expand> 65 </expand>
104 <has_text_matching expression=">EDGE_.+"/> 103 <has_text_matching expression=">EDGE_.+"/>
105 </assert_contents> 104 </assert_contents>
106 </output> 105 </output>
107 <output name="out_ags"> 106 <output name="out_ags">
108 <assert_contents> 107 <assert_contents>
109 <has_n_lines n="2"/> 108 <has_n_lines n="3"/>
110 <has_text_matching expression="S.+"/> 109 <has_text_matching expression="H.+"/>
110 <has_text_matching expression="S.+"/>
111 <has_text_matching expression="P.+"/>
111 </assert_contents> 112 </assert_contents>
112 </output> 113 </output>
113 <output name="out_cn"> 114 <output name="out_cn">
114 <assert_contents> 115 <assert_contents>
115 <has_n_lines n="18"/> 116 <has_n_lines n="18"/>
124 </output> 125 </output>
125 </test> 126 </test>
126 <!-- #2 single, separate, fastq, custom parameters --> 127 <!-- #2 single, separate, fastq, custom parameters -->
127 <test expect_num_outputs="9"> 128 <test expect_num_outputs="9">
128 <conditional name="singlePaired"> 129 <conditional name="singlePaired">
129 <param name="sPaired" value="paired"/> 130 <param name="sPaired" value="paired_collection"/>
130 <param name="input1" value="ecoli_1K_1.fastq.gz"/> 131 <param name="input">
131 <param name="input2" value="ecoli_1K_2.fastq.gz"/> 132 <collection type="list:paired">
133 <element name="ecoli_1K">
134 <collection type="paired">
135 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
136 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
137 </collection>
138 </element>
139 </collection>
140 </param>
132 </conditional> 141 </conditional>
133 <param name="mode_sel" value="--isolate,--disable-rr,--iontorrent"/> 142 <param name="mode_sel" value="--isolate,--disable-rr,--iontorrent"/>
134 <conditional name="cov_cond"> 143 <conditional name="cov_cond">
135 <param name="cov_cutoff" value="auto"/> 144 <param name="cov_cutoff" value="auto"/>
136 </conditional> 145 </conditional>
146 <has_text_matching expression=">EDGE_.+"/> 155 <has_text_matching expression=">EDGE_.+"/>
147 </assert_contents> 156 </assert_contents>
148 </output> 157 </output>
149 <output name="out_ags"> 158 <output name="out_ags">
150 <assert_contents> 159 <assert_contents>
151 <has_n_lines n="1"/> 160 <has_n_lines n="2"/>
161 <has_text_matching expression="H.+"/>
152 <has_text_matching expression="S.+"/> 162 <has_text_matching expression="S.+"/>
153 </assert_contents> 163 </assert_contents>
154 </output> 164 </output>
155 <output name="out_cn"> 165 <output name="out_cn">
156 <assert_contents> 166 <assert_contents>
193 </test> 203 </test>
194 <!-- #3 single, separate, fasta, default parameters --> 204 <!-- #3 single, separate, fasta, default parameters -->
195 <test expect_num_outputs="4"> 205 <test expect_num_outputs="4">
196 <param name="operation_mode" value="--only-assembler"/> 206 <param name="operation_mode" value="--only-assembler"/>
197 <conditional name="singlePaired"> 207 <conditional name="singlePaired">
198 <param name="sPaired" value="paired"/> 208 <param name="sPaired" value="paired_collection"/>
199 <param name="input1" value="ecoli_1K_1.fastq.gz"/> 209 <param name="input">
200 <param name="input2" value="ecoli_1K_2.fastq.gz"/> 210 <collection type="list:paired">
211 <element name="ecoli_1K">
212 <collection type="paired">
213 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
214 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
215 </collection>
216 </element>
217 </collection>
218 </param>
201 </conditional> 219 </conditional>
202 <output name="out_ag"> 220 <output name="out_ag">
203 <assert_contents> 221 <assert_contents>
204 <has_n_lines n="36"/> 222 <has_n_lines n="36"/>
205 <has_text_matching expression=">EDGE_.+"/> 223 <has_text_matching expression=">EDGE_.+"/>
206 </assert_contents> 224 </assert_contents>
207 </output> 225 </output>
208 <output name="out_ags"> 226 <output name="out_ags">
209 <assert_contents> 227 <assert_contents>
210 <has_n_lines n="2"/> 228 <has_n_lines n="3"/>
211 <has_text_matching expression="S.+"/> 229 <has_text_matching expression="H.+"/>
230 <has_text_matching expression="S.+"/>
231 <has_text_matching expression="P.+"/>
212 </assert_contents> 232 </assert_contents>
213 </output> 233 </output>
214 <output name="out_cn"> 234 <output name="out_cn">
215 <assert_contents> 235 <assert_contents>
216 <has_n_lines n="18"/> 236 <has_n_lines n="18"/>
231 <param name="input1" value="ecoli_1K.fastq.gz"/> 251 <param name="input1" value="ecoli_1K.fastq.gz"/>
232 </conditional> 252 </conditional>
233 <conditional name="additional_reads"> 253 <conditional name="additional_reads">
234 <param name="selector" value="true"/> 254 <param name="selector" value="true"/>
235 <conditional name="singlePaired"> 255 <conditional name="singlePaired">
236 <param name="sPaired" value="paired"/> 256 <param name="sPaired" value="paired_collection"/>
237 <param name="input1" value="ecoli_1K_1.fastq.gz"/> 257 <param name="input">
238 <param name="input2" value="ecoli_1K_2.fastq.gz"/> 258 <collection type="list:paired">
259 <element name="ecoli_1K">
260 <collection type="paired">
261 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
262 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
263 </collection>
264 </element>
265 </collection>
266 </param>
239 </conditional> 267 </conditional>
240 </conditional> 268 </conditional>
241 <param name="mode_sel" value="--careful"/> 269 <param name="mode_sel" value="--careful"/>
242 <output name="out_ag"> 270 <output name="out_ag">
243 <assert_contents> 271 <assert_contents>
245 <has_text_matching expression=">EDGE_.+"/> 273 <has_text_matching expression=">EDGE_.+"/>
246 </assert_contents> 274 </assert_contents>
247 </output> 275 </output>
248 <output name="out_ags"> 276 <output name="out_ags">
249 <assert_contents> 277 <assert_contents>
250 <has_n_lines n="2"/> 278 <has_n_lines n="3"/>
251 <has_text_matching expression="S.+"/> 279 <has_text_matching expression="H.+"/>
280 <has_text_matching expression="S.+"/>
281 <has_text_matching expression="P.+"/>
252 </assert_contents> 282 </assert_contents>
253 </output> 283 </output>
254 <output name="out_cn"> 284 <output name="out_cn">
255 <assert_contents> 285 <assert_contents>
256 <has_n_lines n="18"/> 286 <has_n_lines n="18"/>
272 <param name="input1" value="ecoli_1K.fastq.gz"/> 302 <param name="input1" value="ecoli_1K.fastq.gz"/>
273 </conditional> 303 </conditional>
274 <conditional name="additional_reads"> 304 <conditional name="additional_reads">
275 <param name="selector" value="true"/> 305 <param name="selector" value="true"/>
276 <conditional name="singlePaired"> 306 <conditional name="singlePaired">
277 <param name="sPaired" value="paired"/> 307 <param name="sPaired" value="paired_collection"/>
278 <param name="input1" value="ecoli_1K_1.fastq.gz"/> 308 <param name="input">
279 <param name="input2" value="ecoli_1K_2.fastq.gz"/> 309 <collection type="list:paired">
310 <element name="ecoli_1K">
311 <collection type="paired">
312 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
313 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
314 </collection>
315 </element>
316 </collection>
317 </param>
280 </conditional> 318 </conditional>
281 </conditional> 319 </conditional>
282 <param name="mode_sel" value="--careful"/> 320 <param name="mode_sel" value="--careful"/>
283 <output name="out_ag"> 321 <output name="out_ag">
284 <assert_contents> 322 <assert_contents>
286 <has_text_matching expression=">EDGE_.+"/> 324 <has_text_matching expression=">EDGE_.+"/>
287 </assert_contents> 325 </assert_contents>
288 </output> 326 </output>
289 <output name="out_ags"> 327 <output name="out_ags">
290 <assert_contents> 328 <assert_contents>
291 <has_n_lines n="2"/> 329 <has_n_lines n="3"/>
292 <has_text_matching expression="S.+"/> 330 <has_text_matching expression="H.+"/>
331 <has_text_matching expression="S.+"/>
332 <has_text_matching expression="P.+"/>
293 </assert_contents> 333 </assert_contents>
294 </output> 334 </output>
295 <output name="out_cn"> 335 <output name="out_cn">
296 <assert_contents> 336 <assert_contents>
297 <has_n_lines n="18"/> 337 <has_n_lines n="18"/>
313 <param name="input1" value="ecoli_1K.fastq.gz"/> 353 <param name="input1" value="ecoli_1K.fastq.gz"/>
314 </conditional> 354 </conditional>
315 <param name="mode_sel" value="--careful"/> 355 <param name="mode_sel" value="--careful"/>
316 <param name="optional_output" value="cr,l"/> 356 <param name="optional_output" value="cr,l"/>
317 <output_collection name="out_cr" type="list" count="3"> 357 <output_collection name="out_cr" type="list" count="3">
318 <element name="ecoli_1K.fastq.gz_1.00.0_0"> 358 <element name="ecoli_1K.fastq.gz_100.0_0">
319 <assert_contents> 359 <assert_contents>
320 <has_size value="130317" delta="5000"/> 360 <has_size value="130317" delta="7000"/>
321 </assert_contents> 361 </assert_contents>
322 </element> 362 </element>
323 <element name="ecoli_1K.fastq.gz_2.00.0_0"> 363 <element name="ecoli_1K.fastq.gz_200.0_0">
324 <assert_contents> 364 <assert_contents>
325 <has_size value="130317" delta="5000"/> 365 <has_size value="130317" delta="7000"/>
326 </assert_contents> 366 </assert_contents>
327 </element> 367 </element>
328 <element name="ecoli_1K.fastq.gz__unpaired.00.0_0"> 368 <element name="ecoli_1K.fastq.gz__unpaired00.0_0">
329 <assert_contents> 369 <assert_contents>
330 <has_size value="20" delta="5"/> 370 <has_size value="20" delta="5"/>
331 </assert_contents> 371 </assert_contents>
332 </element> 372 </element>
333 </output_collection> 373 </output_collection>
345 <param name="input1" value="ecoli_1K.fastq.gz"/> 385 <param name="input1" value="ecoli_1K.fastq.gz"/>
346 </conditional> 386 </conditional>
347 <param name="mode_sel" value="--careful,--sc"/> 387 <param name="mode_sel" value="--careful,--sc"/>
348 <param name="optional_output" value="cr,l"/> 388 <param name="optional_output" value="cr,l"/>
349 <output_collection name="out_cr" type="list" count="3"> 389 <output_collection name="out_cr" type="list" count="3">
350 <element name="ecoli_1K.fastq.gz_1.00.0_0"> 390 <element name="ecoli_1K.fastq.gz_100.0_0">
351 <assert_contents> 391 <assert_contents>
352 <has_size value="130317" delta="5000"/> 392 <has_size value="130317" delta="7000"/>
353 </assert_contents> 393 </assert_contents>
354 </element> 394 </element>
355 <element name="ecoli_1K.fastq.gz_2.00.0_0"> 395 <element name="ecoli_1K.fastq.gz_200.0_0">
356 <assert_contents> 396 <assert_contents>
357 <has_size value="130317" delta="5000"/> 397 <has_size value="130317" delta="7000"/>
358 </assert_contents> 398 </assert_contents>
359 </element> 399 </element>
360 <element name="ecoli_1K.fastq.gz__unpaired.00.0_0"> 400 <element name="ecoli_1K.fastq.gz__unpaired00.0_0">
361 <assert_contents> 401 <assert_contents>
362 <has_size value="20" delta="5"/> 402 <has_size value="20" delta="5"/>
363 </assert_contents> 403 </assert_contents>
364 </element> 404 </element>
365 </output_collection> 405 </output_collection>
378 </conditional> 418 </conditional>
379 <param name="mode_sel" value="--sc"/> 419 <param name="mode_sel" value="--sc"/>
380 <output name="out_ag"> 420 <output name="out_ag">
381 <assert_contents> 421 <assert_contents>
382 <has_n_lines n="36"/> 422 <has_n_lines n="36"/>
383 <has_text_matching expression=">EDGE_7_length_1000_cov_140.639153"/> 423 <has_text_matching expression=">EDGE_[0-9]+_length_[0-9]+_cov_[0-9]+\.[0-9]+"/>
384 </assert_contents> 424 </assert_contents>
385 </output> 425 </output>
386 <output name="out_ags"> 426 <output name="out_ags">
387 <assert_contents> 427 <assert_contents>
388 <has_n_lines n="2"/> 428 <has_n_lines n="3"/>
389 <has_text_matching expression="S.+"/> 429 <has_text_matching expression="H.+"/>
430 <has_text_matching expression="S.+"/>
431 <has_text_matching expression="P.+"/>
390 </assert_contents> 432 </assert_contents>
391 </output> 433 </output>
392 <output name="out_cn"> 434 <output name="out_cn">
393 <assert_contents> 435 <assert_contents>
394 <has_n_lines n="18"/> 436 <has_n_lines n="18"/>
409 <param name="sPaired" value="paired_interlaced"/> 451 <param name="sPaired" value="paired_interlaced"/>
410 <param name="input1" value="ecoli_1K.fastq.gz"/> 452 <param name="input1" value="ecoli_1K.fastq.gz"/>
411 </conditional> 453 </conditional>
412 <param name="optional_output" value="cr,l"/> 454 <param name="optional_output" value="cr,l"/>
413 <output_collection name="out_cr" type="list" count="3"> 455 <output_collection name="out_cr" type="list" count="3">
414 <element name="ecoli_1K.fastq.gz_1.00.0_0"> 456 <element name="ecoli_1K.fastq.gz_100.0_0">
415 <assert_contents> 457 <assert_contents>
416 <has_size value="130317" delta="5000"/> 458 <has_size value="130317" delta="7000"/>
417 </assert_contents> 459 </assert_contents>
418 </element> 460 </element>
419 <element name="ecoli_1K.fastq.gz_2.00.0_0"> 461 <element name="ecoli_1K.fastq.gz_200.0_0">
420 <assert_contents> 462 <assert_contents>
421 <has_size value="130317" delta="5000"/> 463 <has_size value="130317" delta="7000"/>
422 </assert_contents> 464 </assert_contents>
423 </element> 465 </element>
424 <element name="ecoli_1K.fastq.gz__unpaired.00.0_0"> 466 <element name="ecoli_1K.fastq.gz__unpaired00.0_0">
425 <assert_contents> 467 <assert_contents>
426 <has_size value="20" delta="5"/> 468 <has_size value="20" delta="5"/>
427 </assert_contents> 469 </assert_contents>
428 </element> 470 </element>
429 </output_collection> 471 </output_collection>
441 <param name="input1" value="ecoli_1K.fastq.gz"/> 483 <param name="input1" value="ecoli_1K.fastq.gz"/>
442 </conditional> 484 </conditional>
443 <param name="mode_sel" value="--sc"/> 485 <param name="mode_sel" value="--sc"/>
444 <param name="optional_output" value="cr,l"/> 486 <param name="optional_output" value="cr,l"/>
445 <output_collection name="out_cr" type="list" count="3"> 487 <output_collection name="out_cr" type="list" count="3">
446 <element name="ecoli_1K.fastq.gz_1.00.0_0"> 488 <element name="ecoli_1K.fastq.gz_100.0_0">
447 <assert_contents> 489 <assert_contents>
448 <has_size value="130317" delta="5000"/> 490 <has_size value="130317" delta="7000"/>
449 </assert_contents> 491 </assert_contents>
450 </element> 492 </element>
451 <element name="ecoli_1K.fastq.gz_2.00.0_0"> 493 <element name="ecoli_1K.fastq.gz_200.0_0">
452 <assert_contents> 494 <assert_contents>
453 <has_size value="130317" delta="5000"/> 495 <has_size value="130317" delta="7000"/>
454 </assert_contents> 496 </assert_contents>
455 </element> 497 </element>
456 <element name="ecoli_1K.fastq.gz__unpaired.00.0_0"> 498 <element name="ecoli_1K.fastq.gz__unpaired00.0_0">
457 <assert_contents> 499 <assert_contents>
458 <has_size value="20" delta="5"/> 500 <has_size value="20" delta="5"/>
459 </assert_contents> 501 </assert_contents>
460 </element> 502 </element>
461 </output_collection> 503 </output_collection>
478 <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106"/> 520 <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106"/>
479 </assert_contents> 521 </assert_contents>
480 </output> 522 </output>
481 <output name="out_ags"> 523 <output name="out_ags">
482 <assert_contents> 524 <assert_contents>
483 <has_n_lines n="2"/> 525 <has_n_lines n="3"/>
484 <has_text_matching expression="S.+"/> 526 <has_text_matching expression="H.+"/>
527 <has_text_matching expression="S.+"/>
528 <has_text_matching expression="P.+"/>
485 </assert_contents> 529 </assert_contents>
486 </output> 530 </output>
487 <output name="out_cn"> 531 <output name="out_cn">
488 <assert_contents> 532 <assert_contents>
489 <has_n_lines n="18"/> 533 <has_n_lines n="18"/>
498 </output> 542 </output>
499 </test> 543 </test>
500 <!-- #12 --> 544 <!-- #12 -->
501 <test expect_num_outputs="4"> 545 <test expect_num_outputs="4">
502 <conditional name="singlePaired"> 546 <conditional name="singlePaired">
503 <param name="sPaired" value="paired"/> 547 <param name="sPaired" value="paired_collection"/>
504 <param name="input1" value="ecoli_1K_1.fastq.gz"/> 548 <param name="input">
505 <param name="input2" value="ecoli_1K_2.fastq.gz"/> 549 <collection type="list:paired">
550 <element name="ecoli_1K">
551 <collection type="paired">
552 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
553 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
554 </collection>
555 </element>
556 </collection>
557 </param>
506 </conditional> 558 </conditional>
507 <param name="mode_sel" value="--sc,--careful"/> 559 <param name="mode_sel" value="--sc,--careful"/>
508 <output name="out_ag"> 560 <output name="out_ag">
509 <assert_contents> 561 <assert_contents>
510 <has_n_lines n="36"/> 562 <has_n_lines n="36"/>
511 <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106"/> 563 <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106"/>
512 </assert_contents> 564 </assert_contents>
513 </output> 565 </output>
514 <output name="out_ags"> 566 <output name="out_ags">
515 <assert_contents> 567 <assert_contents>
516 <has_n_lines n="2"/> 568 <has_n_lines n="3"/>
517 <has_text_matching expression="S.+"/> 569 <has_text_matching expression="H.+"/>
570 <has_text_matching expression="S.+"/>
571 <has_text_matching expression="P.+"/>
518 </assert_contents> 572 </assert_contents>
519 </output> 573 </output>
520 <output name="out_cn"> 574 <output name="out_cn">
521 <assert_contents> 575 <assert_contents>
522 <has_n_lines n="18"/> 576 <has_n_lines n="18"/>
532 </test> 586 </test>
533 <!-- #13 --> 587 <!-- #13 -->
534 <test expect_num_outputs="4"> 588 <test expect_num_outputs="4">
535 <param name="operation_mode" value="--only-assembler"/> 589 <param name="operation_mode" value="--only-assembler"/>
536 <conditional name="singlePaired"> 590 <conditional name="singlePaired">
537 <param name="sPaired" value="paired"/> 591 <param name="sPaired" value="paired_collection"/>
538 <param name="input1" value="ecoli_1K_1.fastq.gz"/> 592 <param name="input">
539 <param name="input2" value="ecoli_1K_2.fastq.gz"/> 593 <collection type="list:paired">
594 <element name="ecoli_1K">
595 <collection type="paired">
596 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
597 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
598 </collection>
599 </element>
600 </collection>
601 </param>
540 </conditional> 602 </conditional>
541 <param name="mode_sel" value="--sc,--careful"/> 603 <param name="mode_sel" value="--sc,--careful"/>
542 <output name="out_ag"> 604 <output name="out_ag">
543 <assert_contents> 605 <assert_contents>
544 <has_n_lines n="36"/> 606 <has_n_lines n="36"/>
545 <has_text_matching expression=">EDGE\_.+"/> 607 <has_text_matching expression=">EDGE\_.+"/>
546 </assert_contents> 608 </assert_contents>
547 </output> 609 </output>
548 <output name="out_ags"> 610 <output name="out_ags">
549 <assert_contents> 611 <assert_contents>
550 <has_n_lines n="2"/> 612 <has_n_lines n="3"/>
551 <has_text_matching expression="S.+"/> 613 <has_text_matching expression="H.+"/>
614 <has_text_matching expression="S.+"/>
615 <has_text_matching expression="P.+"/>
552 </assert_contents> 616 </assert_contents>
553 </output> 617 </output>
554 <output name="out_cn"> 618 <output name="out_cn">
555 <assert_contents> 619 <assert_contents>
556 <has_n_lines n="18"/> 620 <has_n_lines n="18"/>
588 <has_text_matching expression=">EDGE_.+"/> 652 <has_text_matching expression=">EDGE_.+"/>
589 </assert_contents> 653 </assert_contents>
590 </output> 654 </output>
591 <output name="out_ags"> 655 <output name="out_ags">
592 <assert_contents> 656 <assert_contents>
593 <has_n_lines n="2"/> 657 <has_n_lines n="3"/>
594 <has_text_matching expression="S.+"/> 658 <has_text_matching expression="H.+"/>
659 <has_text_matching expression="S.+"/>
660 <has_text_matching expression="P.+"/>
595 </assert_contents> 661 </assert_contents>
596 </output> 662 </output>
597 <output name="out_cn"> 663 <output name="out_cn">
598 <assert_contents> 664 <assert_contents>
599 <has_n_lines n="18"/> 665 <has_n_lines n="18"/>
608 </output> 674 </output>
609 </test> 675 </test>
610 <!-- #15 mate-pair reads orientation rf--> 676 <!-- #15 mate-pair reads orientation rf-->
611 <test expect_num_outputs="4"> 677 <test expect_num_outputs="4">
612 <conditional name="singlePaired"> 678 <conditional name="singlePaired">
613 <param name="sPaired" value="paired"/> 679 <param name="sPaired" value="paired_collection"/>
614 <param name="input1" value="ecoli_1K_1.fastq.gz"/> 680 <param name="input">
615 <param name="input2" value="ecoli_1K_2.fastq.gz"/> 681 <collection type="list:paired">
682 <element name="ecoli_1K">
683 <collection type="paired">
684 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
685 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
686 </collection>
687 </element>
688 </collection>
689 </param>
616 <param name="type_paired" value="hqmp"/> 690 <param name="type_paired" value="hqmp"/>
617 <param name="orientation" value="rf"/> 691 <param name="orientation" value="rf"/>
618 </conditional> 692 </conditional>
619 <output name="out_ag"> 693 <output name="out_ag">
620 <assert_contents> 694 <assert_contents>
622 <has_text_matching expression=">EDGE_.+"/> 696 <has_text_matching expression=">EDGE_.+"/>
623 </assert_contents> 697 </assert_contents>
624 </output> 698 </output>
625 <output name="out_ags"> 699 <output name="out_ags">
626 <assert_contents> 700 <assert_contents>
627 <has_n_lines n="1"/> 701 <has_n_lines n="2"/>
702 <has_text_matching expression="H.+"/>
703 <has_text_matching expression="S.+"/>
628 </assert_contents> 704 </assert_contents>
629 </output> 705 </output>
630 <output name="out_cn"> 706 <output name="out_cn">
631 <assert_contents> 707 <assert_contents>
632 <has_n_lines n="18"/> 708 <has_n_lines n="18"/>
661 <has_text_matching expression=">EDGE_.+"/> 737 <has_text_matching expression=">EDGE_.+"/>
662 </assert_contents> 738 </assert_contents>
663 </output> 739 </output>
664 <output name="out_ags"> 740 <output name="out_ags">
665 <assert_contents> 741 <assert_contents>
666 <has_n_lines n="2"/> 742 <has_n_lines n="3"/>
667 <has_text_matching expression="S.+"/> 743 <has_text_matching expression="H.+"/>
744 <has_text_matching expression="S.+"/>
745 <has_text_matching expression="P.+"/>
668 </assert_contents> 746 </assert_contents>
669 </output> 747 </output>
670 <output name="out_cn"> 748 <output name="out_cn">
671 <assert_contents> 749 <assert_contents>
672 <has_n_lines n="18"/> 750 <has_n_lines n="18"/>