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comparison ngsplot.xml @ 0:3ca58369469c draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
author artbio
date Wed, 06 Dec 2017 19:01:53 -0500
parents
children 4dd92ce61a5c
comparison
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-1:000000000000 0:3ca58369469c
1 <tool id="ngsplot" name="ngsplot" version="0.1.0">
2 <description>visualize NGS samples at functional genomic regions - beta</description>
3 <requirements>
4 <requirement type="package" version="1.17.1=r3.3.2_1">r-catools</requirement>
5 <requirement type="package" version="1.3.4">r-domc</requirement>
6 <requirement type="package" version="1.42.0">bioconductor-bsgenome</requirement>
7 <!-- <requirement type="package" version="1.26.1">bioconductor-rsamtools</requirement> -->
8 <requirement type="package" version="1.32.0">bioconductor-shortread</requirement>
9 <!-- <requirement type="package" version="0.16.1=r3.2.2_0">bioconductor-biocgenerics</requirement> -->
10 </requirements>
11
12 <command><![CDATA[
13 export NGSPLOT="$__tool_directory__" &&
14 #if $numsamples.numsamples2 == "1":
15 perl "$__tool_directory__"/runNGSplot.pl
16 $genome_name
17 $genomic_region_source_type.genomic_region
18 $genomic_region_source_type.further_information
19 $genomic_region_source_type.interval_size
20 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
21 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
22 $numsamples.numsamples2
23 $numsamples.usepair.usepair1
24
25 $numsamples.usepair.bamfile1
26 $numsamples.usepair.reffile1
27 $numsamples.usepair.genelist1.usegenelist1
28 $numsamples.usepair.genelist1.genelist1
29 $numsamples.usepair.title1
30 $numsamples.usepair.fraglen1
31 $numsamples.usepair.linecol1
32
33 $gene_database
34 $randomly_sample
35 $GO.gene_order
36 $GO.KNC
37 $GO.MIT
38 $GO.NRS
39 $chunk_size
40 $quality_requirement
41 $standard_error
42 $radius_size
43 $flooding_fraction
44 $smooth_method
45 $shaded_area
46 $out_zip $out_avg_png $out_hm_png
47
48 #else if $numsamples.numsamples2 == "2":
49 perl "$__tool_directory__"/runNGSplot.pl
50 $genome_name
51 $genomic_region_source_type.genomic_region
52 $genomic_region_source_type.further_information
53 $genomic_region_source_type.interval_size
54 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
55 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
56 $numsamples.numsamples2
57 $numsamples.usepair.usepair1
58
59 $numsamples.usepair.bamfile1
60 $numsamples.usepair.reffile1
61 $numsamples.usepair.genelist1.usegenelist1
62 $numsamples.usepair.genelist1.genelist1
63 $numsamples.usepair.title1
64 $numsamples.usepair.fraglen1
65 $numsamples.usepair.linecol1
66
67 $numsamples.usepair.bamfile2
68 $numsamples.usepair.reffile2
69 $numsamples.usepair.genelist2.usegenelist2
70 $numsamples.usepair.genelist2.genelist2
71 $numsamples.usepair.title2
72 $numsamples.usepair.fraglen2
73 $numsamples.usepair.linecol2
74
75 $gene_database
76 $randomly_sample
77 $GO.gene_order
78 $GO.KNC
79 $GO.MIT
80 $GO.NRS
81 $chunk_size
82 $quality_requirement
83 $standard_error
84 $radius_size
85 $flooding_fraction
86 $smooth_method
87 $shaded_area
88 $out_zip $out_avg_png $out_hm_png
89
90 #else if $numsamples.numsamples2 == "3":
91 perl "$__tool_directory__"/runNGSplot.pl
92 $genome_name
93 $genomic_region_source_type.genomic_region
94 $genomic_region_source_type.further_information
95 $genomic_region_source_type.interval_size
96 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
97 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
98 $numsamples.numsamples2
99 $numsamples.usepair.usepair1
100
101 $numsamples.usepair.bamfile1
102 $numsamples.usepair.reffile1
103 $numsamples.usepair.genelist1.usegenelist1
104 $numsamples.usepair.genelist1.genelist1
105 $numsamples.usepair.title1
106 $numsamples.usepair.fraglen1
107 $numsamples.usepair.linecol1
108
109 $numsamples.usepair.bamfile2
110 $numsamples.usepair.reffile2
111 $numsamples.usepair.genelist2.usegenelist2
112 $numsamples.usepair.genelist2.genelist2
113 $numsamples.usepair.title2
114 $numsamples.usepair.fraglen2
115 $numsamples.usepair.linecol2
116
117 $numsamples.usepair.bamfile3
118 $numsamples.usepair.reffile3
119 $numsamples.usepair.genelist3.usegenelist3
120 $numsamples.usepair.genelist3.genelist3
121 $numsamples.usepair.title3
122 $numsamples.usepair.fraglen3
123 $numsamples.usepair.linecol3
124
125 $gene_database
126 $randomly_sample
127 $GO.gene_order
128 $GO.KNC
129 $GO.MIT
130 $GO.NRS
131 $chunk_size
132 $quality_requirement
133 $standard_error
134 $radius_size
135 $flooding_fraction
136 $smooth_method
137 $shaded_area
138 $out_zip $out_avg_png $out_hm_png
139
140 #else if $numsamples.numsamples2 == "4":
141 perl "$__tool_directory__"/runNGSplot.pl
142 $genome_name
143 $genomic_region_source_type.genomic_region
144 $genomic_region_source_type.further_information
145 $genomic_region_source_type.interval_size
146 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
147 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
148 $numsamples.numsamples2
149 $numsamples.usepair.usepair1
150
151 $numsamples.usepair.bamfile1
152 $numsamples.usepair.reffile1
153 $numsamples.usepair.genelist1.usegenelist1
154 $numsamples.usepair.genelist1.genelist1
155 $numsamples.usepair.title1
156 $numsamples.usepair.fraglen1
157 $numsamples.usepair.linecol1
158
159 $numsamples.usepair.bamfile2
160 $numsamples.usepair.reffile2
161 $numsamples.usepair.genelist2.usegenelist2
162 $numsamples.usepair.genelist2.genelist2
163 $numsamples.usepair.title2
164 $numsamples.usepair.fraglen2
165 $numsamples.usepair.linecol2
166
167 $numsamples.usepair.bamfile3
168 $numsamples.usepair.reffile3
169 $numsamples.usepair.genelist3.usegenelist3
170 $numsamples.usepair.genelist3.genelist3
171 $numsamples.usepair.title3
172 $numsamples.usepair.fraglen3
173 $numsamples.usepair.linecol3
174
175 $numsamples.usepair.bamfile4
176 $numsamples.usepair.reffile4
177 $numsamples.usepair.genelist4.usegenelist4
178 $numsamples.usepair.genelist4.genelist4
179 $numsamples.usepair.title4
180 $numsamples.usepair.fraglen4
181 $numsamples.usepair.linecol4
182
183 $gene_database
184 $randomly_sample
185 $GO.gene_order
186 $GO.KNC
187 $GO.MIT
188 $GO.NRS
189 $chunk_size
190 $quality_requirement
191 $standard_error
192 $radius_size
193 $flooding_fraction
194 $smooth_method
195 $shaded_area
196 $out_zip $out_avg_png $out_hm_png
197
198 #else if $numsamples.numsamples2 == "5":
199 perl "$__tool_directory__"/runNGSplot.pl
200 $genome_name
201 $genomic_region_source_type.genomic_region
202 $genomic_region_source_type.further_information
203 $genomic_region_source_type.interval_size
204 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
205 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
206 $numsamples.numsamples2
207 $numsamples.usepair.usepair1
208
209 $numsamples.usepair.bamfile1
210 $numsamples.usepair.reffile1
211 $numsamples.usepair.genelist1.usegenelist1
212 $numsamples.usepair.genelist1.genelist1
213 $numsamples.usepair.title1
214 $numsamples.usepair.fraglen1
215 $numsamples.usepair.linecol1
216
217 $numsamples.usepair.bamfile2
218 $numsamples.usepair.reffile2
219 $numsamples.usepair.genelist2.usegenelist2
220 $numsamples.usepair.genelist2.genelist2
221 $numsamples.usepair.title2
222 $numsamples.usepair.fraglen2
223 $numsamples.usepair.linecol2
224
225 $numsamples.usepair.bamfile3
226 $numsamples.usepair.reffile3
227 $numsamples.usepair.genelist3.usegenelist3
228 $numsamples.usepair.genelist3.genelist3
229 $numsamples.usepair.title3
230 $numsamples.usepair.fraglen3
231 $numsamples.usepair.linecol3
232
233 $numsamples.usepair.bamfile4
234 $numsamples.usepair.reffile4
235 $numsamples.usepair.genelist4.usegenelist4
236 $numsamples.usepair.genelist4.genelist4
237 $numsamples.usepair.title4
238 $numsamples.usepair.fraglen4
239 $numsamples.usepair.linecol4
240
241 $numsamples.usepair.bamfile5
242 $numsamples.usepair.reffile5
243 $numsamples.usepair.genelist5.usegenelist5
244 $numsamples.usepair.genelist5.genelist5
245 $numsamples.usepair.title5
246 $numsamples.usepair.fraglen5
247 $numsamples.usepair.linecol5
248
249 $gene_database
250 $randomly_sample
251 $GO.gene_order
252 $GO.KNC
253 $GO.MIT
254 $GO.NRS
255 $chunk_size
256 $quality_requirement
257 $standard_error
258 $radius_size
259 $flooding_fraction
260 $smooth_method
261 $shaded_area
262 $out_zip $out_avg_png $out_hm_png
263
264 #else if $numsamples.numsamples2 == "6":
265 perl "$__tool_directory__"/runNGSplot.pl
266 $genome_name
267 $genomic_region_source_type.genomic_region
268 $genomic_region_source_type.further_information
269 $genomic_region_source_type.interval_size
270 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
271 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
272 $numsamples.numsamples2
273 $numsamples.usepair.usepair1
274
275 $numsamples.usepair.bamfile1
276 $numsamples.usepair.reffile1
277 $numsamples.usepair.genelist1.usegenelist1
278 $numsamples.usepair.genelist1.genelist1
279 $numsamples.usepair.title1
280 $numsamples.usepair.fraglen1
281 $numsamples.usepair.linecol1
282
283 $numsamples.usepair.bamfile2
284 $numsamples.usepair.reffile2
285 $numsamples.usepair.genelist2.usegenelist2
286 $numsamples.usepair.genelist2.genelist2
287 $numsamples.usepair.title2
288 $numsamples.usepair.fraglen2
289 $numsamples.usepair.linecol2
290
291 $numsamples.usepair.bamfile3
292 $numsamples.usepair.reffile3
293 $numsamples.usepair.genelist3.usegenelist3
294 $numsamples.usepair.genelist3.genelist3
295 $numsamples.usepair.title3
296 $numsamples.usepair.fraglen3
297 $numsamples.usepair.linecol3
298
299 $numsamples.usepair.bamfile4
300 $numsamples.usepair.reffile4
301 $numsamples.usepair.genelist4.usegenelist4
302 $numsamples.usepair.genelist4.genelist4
303 $numsamples.usepair.title4
304 $numsamples.usepair.fraglen4
305 $numsamples.usepair.linecol4
306
307 $numsamples.usepair.bamfile5
308 $numsamples.usepair.reffile5
309 $numsamples.usepair.genelist5.usegenelist5
310 $numsamples.usepair.genelist5.genelist5
311 $numsamples.usepair.title5
312 $numsamples.usepair.fraglen5
313 $numsamples.usepair.linecol5
314
315 $numsamples.usepair.bamfile6
316 $numsamples.usepair.reffile6
317 $numsamples.usepair.genelist6.usegenelist6
318 $numsamples.usepair.genelist6.genelist6
319 $numsamples.usepair.title6
320 $numsamples.usepair.fraglen6
321 $numsamples.usepair.linecol6
322
323 $gene_database
324 $randomly_sample
325 $GO.gene_order
326 $GO.KNC
327 $GO.MIT
328 $GO.NRS
329 $chunk_size
330 $quality_requirement
331 $standard_error
332 $radius_size
333 $flooding_fraction
334 $smooth_method
335 $shaded_area
336 $out_zip $out_avg_png $out_hm_png
337
338 #else if $numsamples.numsamples2 == "7":
339 perl "$__tool_directory__"/runNGSplot.pl
340 $genome_name
341 $genomic_region_source_type.genomic_region
342 $genomic_region_source_type.further_information
343 $genomic_region_source_type.interval_size
344 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
345 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
346 $numsamples.numsamples2
347 $numsamples.usepair.usepair1
348
349 $numsamples.usepair.bamfile1
350 $numsamples.usepair.reffile1
351 $numsamples.usepair.genelist1.usegenelist1
352 $numsamples.usepair.genelist1.genelist1
353 $numsamples.usepair.title1
354 $numsamples.usepair.fraglen1
355 $numsamples.usepair.linecol1
356
357 $numsamples.usepair.bamfile2
358 $numsamples.usepair.reffile2
359 $numsamples.usepair.genelist2.usegenelist2
360 $numsamples.usepair.genelist2.genelist2
361 $numsamples.usepair.title2
362 $numsamples.usepair.fraglen2
363 $numsamples.usepair.linecol2
364
365 $numsamples.usepair.bamfile3
366 $numsamples.usepair.reffile3
367 $numsamples.usepair.genelist3.usegenelist3
368 $numsamples.usepair.genelist3.genelist3
369 $numsamples.usepair.title3
370 $numsamples.usepair.fraglen3
371 $numsamples.usepair.linecol3
372
373 $numsamples.usepair.bamfile4
374 $numsamples.usepair.reffile4
375 $numsamples.usepair.genelist4.usegenelist4
376 $numsamples.usepair.genelist4.genelist4
377 $numsamples.usepair.title4
378 $numsamples.usepair.fraglen4
379 $numsamples.usepair.linecol4
380
381 $numsamples.usepair.bamfile5
382 $numsamples.usepair.reffile5
383 $numsamples.usepair.genelist5.usegenelist5
384 $numsamples.usepair.genelist5.genelist5
385 $numsamples.usepair.title5
386 $numsamples.usepair.fraglen5
387 $numsamples.usepair.linecol5
388
389 $numsamples.usepair.bamfile6
390 $numsamples.usepair.reffile6
391 $numsamples.usepair.genelist6.usegenelist6
392 $numsamples.usepair.genelist6.genelist6
393 $numsamples.usepair.title6
394 $numsamples.usepair.fraglen6
395 $numsamples.usepair.linecol6
396
397 $numsamples.usepair.bamfile7
398 $numsamples.usepair.reffile7
399 $numsamples.usepair.genelist7.usegenelist7
400 $numsamples.usepair.genelist7.genelist7
401 $numsamples.usepair.title7
402 $numsamples.usepair.fraglen7
403 $numsamples.usepair.linecol7
404
405 $gene_database
406 $randomly_sample
407 $GO.gene_order
408 $GO.KNC
409 $GO.MIT
410 $GO.NRS
411 $chunk_size
412 $quality_requirement
413 $standard_error
414 $radius_size
415 $flooding_fraction
416 $smooth_method
417 $shaded_area
418 $out_zip $out_avg_png $out_hm_png
419
420 #else if $numsamples.numsamples2 == "8":
421 perl "$__tool_directory__"/runNGSplot.pl
422 $genome_name
423 $genomic_region_source_type.genomic_region
424 $genomic_region_source_type.further_information
425 $genomic_region_source_type.interval_size
426 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
427 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
428 $numsamples.numsamples2
429 $numsamples.usepair.usepair1
430
431 $numsamples.usepair.bamfile1
432 $numsamples.usepair.reffile1
433 $numsamples.usepair.genelist1.usegenelist1
434 $numsamples.usepair.genelist1.genelist1
435 $numsamples.usepair.title1
436 $numsamples.usepair.fraglen1
437 $numsamples.usepair.linecol1
438
439 $numsamples.usepair.bamfile2
440 $numsamples.usepair.reffile2
441 $numsamples.usepair.genelist2.usegenelist2
442 $numsamples.usepair.genelist2.genelist2
443 $numsamples.usepair.title2
444 $numsamples.usepair.fraglen2
445 $numsamples.usepair.linecol2
446
447 $numsamples.usepair.bamfile3
448 $numsamples.usepair.reffile3
449 $numsamples.usepair.genelist3.usegenelist3
450 $numsamples.usepair.genelist3.genelist3
451 $numsamples.usepair.title3
452 $numsamples.usepair.fraglen3
453 $numsamples.usepair.linecol3
454
455 $numsamples.usepair.bamfile4
456 $numsamples.usepair.reffile4
457 $numsamples.usepair.genelist4.usegenelist4
458 $numsamples.usepair.genelist4.genelist4
459 $numsamples.usepair.title4
460 $numsamples.usepair.fraglen4
461 $numsamples.usepair.linecol4
462
463 $numsamples.usepair.bamfile5
464 $numsamples.usepair.reffile5
465 $numsamples.usepair.genelist5.usegenelist5
466 $numsamples.usepair.genelist5.genelist5
467 $numsamples.usepair.title5
468 $numsamples.usepair.fraglen5
469 $numsamples.usepair.linecol5
470
471 $numsamples.usepair.bamfile6
472 $numsamples.usepair.reffile6
473 $numsamples.usepair.genelist6.usegenelist6
474 $numsamples.usepair.genelist6.genelist6
475 $numsamples.usepair.title6
476 $numsamples.usepair.fraglen6
477 $numsamples.usepair.linecol6
478
479 $numsamples.usepair.bamfile7
480 $numsamples.usepair.reffile7
481 $numsamples.usepair.genelist7.usegenelist7
482 $numsamples.usepair.genelist7.genelist7
483 $numsamples.usepair.title7
484 $numsamples.usepair.fraglen7
485 $numsamples.usepair.linecol7
486
487 $numsamples.usepair.bamfile8
488 $numsamples.usepair.reffile8
489 $numsamples.usepair.genelist8.usegenelist8
490 $numsamples.usepair.genelist8.genelist8
491 $numsamples.usepair.title8
492 $numsamples.usepair.fraglen8
493 $numsamples.usepair.linecol8
494
495 $gene_database
496 $randomly_sample
497 $GO.gene_order
498 $GO.KNC
499 $GO.MIT
500 $GO.NRS
501 $chunk_size
502 $quality_requirement
503 $standard_error
504 $radius_size
505 $flooding_fraction
506 $smooth_method
507 $shaded_area
508 $out_zip $out_avg_png $out_hm_png
509
510 #else if $numsamples.numsamples2 == "9":
511 perl "$__tool_directory__"/runNGSplot.pl
512 $genome_name
513 $genomic_region_source_type.genomic_region
514 $genomic_region_source_type.further_information
515 $genomic_region_source_type.interval_size
516 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
517 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
518 $numsamples.numsamples2
519 $numsamples.usepair.usepair1
520
521 $numsamples.usepair.bamfile1
522 $numsamples.usepair.reffile1
523 $numsamples.usepair.genelist1.usegenelist1
524 $numsamples.usepair.genelist1.genelist1
525 $numsamples.usepair.title1
526 $numsamples.usepair.fraglen1
527 $numsamples.usepair.linecol1
528
529 $numsamples.usepair.bamfile2
530 $numsamples.usepair.reffile2
531 $numsamples.usepair.genelist2.usegenelist2
532 $numsamples.usepair.genelist2.genelist2
533 $numsamples.usepair.title2
534 $numsamples.usepair.fraglen2
535 $numsamples.usepair.linecol2
536
537 $numsamples.usepair.bamfile3
538 $numsamples.usepair.reffile3
539 $numsamples.usepair.genelist3.usegenelist3
540 $numsamples.usepair.genelist3.genelist3
541 $numsamples.usepair.title3
542 $numsamples.usepair.fraglen3
543 $numsamples.usepair.linecol3
544
545 $numsamples.usepair.bamfile4
546 $numsamples.usepair.reffile4
547 $numsamples.usepair.genelist4.usegenelist4
548 $numsamples.usepair.genelist4.genelist4
549 $numsamples.usepair.title4
550 $numsamples.usepair.fraglen4
551 $numsamples.usepair.linecol4
552
553 $numsamples.usepair.bamfile5
554 $numsamples.usepair.reffile5
555 $numsamples.usepair.genelist5.usegenelist5
556 $numsamples.usepair.genelist5.genelist5
557 $numsamples.usepair.title5
558 $numsamples.usepair.fraglen5
559 $numsamples.usepair.linecol5
560
561 $numsamples.usepair.bamfile6
562 $numsamples.usepair.reffile6
563 $numsamples.usepair.genelist6.usegenelist6
564 $numsamples.usepair.genelist6.genelist6
565 $numsamples.usepair.title6
566 $numsamples.usepair.fraglen6
567 $numsamples.usepair.linecol6
568
569 $numsamples.usepair.bamfile7
570 $numsamples.usepair.reffile7
571 $numsamples.usepair.genelist7.usegenelist7
572 $numsamples.usepair.genelist7.genelist7
573 $numsamples.usepair.title7
574 $numsamples.usepair.fraglen7
575 $numsamples.usepair.linecol7
576
577 $numsamples.usepair.bamfile8
578 $numsamples.usepair.reffile8
579 $numsamples.usepair.genelist8.usegenelist8
580 $numsamples.usepair.genelist8.genelist8
581 $numsamples.usepair.title8
582 $numsamples.usepair.fraglen8
583 $numsamples.usepair.linecol8
584
585 $numsamples.usepair.bamfile9
586 $numsamples.usepair.reffile9
587 $numsamples.usepair.genelist9.usegenelist9
588 $numsamples.usepair.genelist9.genelist9
589 $numsamples.usepair.title9
590 $numsamples.usepair.fraglen9
591 $numsamples.usepair.linecol9
592
593 $gene_database
594 $randomly_sample
595 $GO.gene_order
596 $GO.KNC
597 $GO.MIT
598 $GO.NRS
599 $chunk_size
600 $quality_requirement
601 $standard_error
602 $radius_size
603 $flooding_fraction
604 $smooth_method
605 $shaded_area
606 $out_zip $out_avg_png $out_hm_png
607
608 #else if $numsamples.numsamples2 == "10":
609 perl "$__tool_directory__"/runNGSplot.pl
610 $genome_name
611 $genomic_region_source_type.genomic_region
612 $genomic_region_source_type.further_information
613 $genomic_region_source_type.interval_size
614 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
615 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
616 $numsamples.numsamples2
617 $numsamples.usepair.usepair1
618
619 $numsamples.usepair.bamfile1
620 $numsamples.usepair.reffile1
621 $numsamples.usepair.genelist1.usegenelist1
622 $numsamples.usepair.genelist1.genelist1
623 $numsamples.usepair.title1
624 $numsamples.usepair.fraglen1
625 $numsamples.usepair.linecol1
626
627 $numsamples.usepair.bamfile2
628 $numsamples.usepair.reffile2
629 $numsamples.usepair.genelist2.usegenelist2
630 $numsamples.usepair.genelist2.genelist2
631 $numsamples.usepair.title2
632 $numsamples.usepair.fraglen2
633 $numsamples.usepair.linecol2
634
635 $numsamples.usepair.bamfile3
636 $numsamples.usepair.reffile3
637 $numsamples.usepair.genelist3.usegenelist3
638 $numsamples.usepair.genelist3.genelist3
639 $numsamples.usepair.title3
640 $numsamples.usepair.fraglen3
641 $numsamples.usepair.linecol3
642
643 $numsamples.usepair.bamfile4
644 $numsamples.usepair.reffile4
645 $numsamples.usepair.genelist4.usegenelist4
646 $numsamples.usepair.genelist4.genelist4
647 $numsamples.usepair.title4
648 $numsamples.usepair.fraglen4
649 $numsamples.usepair.linecol4
650
651 $numsamples.usepair.bamfile5
652 $numsamples.usepair.reffile5
653 $numsamples.usepair.genelist5.usegenelist5
654 $numsamples.usepair.genelist5.genelist5
655 $numsamples.usepair.title5
656 $numsamples.usepair.fraglen5
657 $numsamples.usepair.linecol5
658
659 $numsamples.usepair.bamfile6
660 $numsamples.usepair.reffile6
661 $numsamples.usepair.genelist6.usegenelist6
662 $numsamples.usepair.genelist6.genelist6
663 $numsamples.usepair.title6
664 $numsamples.usepair.fraglen6
665 $numsamples.usepair.linecol6
666
667 $numsamples.usepair.bamfile7
668 $numsamples.usepair.reffile7
669 $numsamples.usepair.genelist7.usegenelist7
670 $numsamples.usepair.genelist7.genelist7
671 $numsamples.usepair.title7
672 $numsamples.usepair.fraglen7
673 $numsamples.usepair.linecol7
674
675 $numsamples.usepair.bamfile8
676 $numsamples.usepair.reffile8
677 $numsamples.usepair.genelist8.usegenelist8
678 $numsamples.usepair.genelist8.genelist8
679 $numsamples.usepair.title8
680 $numsamples.usepair.fraglen8
681 $numsamples.usepair.linecol8
682
683 $numsamples.usepair.bamfile9
684 $numsamples.usepair.reffile9
685 $numsamples.usepair.genelist9.usegenelist9
686 $numsamples.usepair.genelist9.genelist9
687 $numsamples.usepair.title9
688 $numsamples.usepair.fraglen9
689 $numsamples.usepair.linecol9
690
691 $numsamples.usepair.bamfile10
692 $numsamples.usepair.reffile10
693 $numsamples.usepair.genelist10.usegenelist10
694 $numsamples.usepair.genelist10.genelist10
695 $numsamples.usepair.title10
696 $numsamples.usepair.fraglen10
697 $numsamples.usepair.linecol10
698
699 $gene_database
700 $randomly_sample
701 $GO.gene_order
702 $GO.KNC
703 $GO.MIT
704 $GO.NRS
705 $chunk_size
706 $quality_requirement
707 $standard_error
708 $radius_size
709 $flooding_fraction
710 $smooth_method
711 $shaded_area
712 $out_zip $out_avg_png $out_hm_png
713
714 #end if
715
716 ]]></command>
717
718 <!-->
719 <-->
720
721 <inputs>
722 <param type="text" value="mm9" name="genome_name" label="Genome" help="(hg19, mm9, rn4, or other genomes supported by your NGS.plot installation)" >
723 </param>
724 <conditional name="genomic_region_source_type">
725 <param type="select" name="genomic_region" label="Genomic region" help="">
726 <option value="tss">TSS</option>
727 <option value="tes">TES</option>
728 <option value="genebody">Genebody</option>
729 <option value="exon">Exon</option>
730 <option value="cgi">CGI</option>
731 <option value="bed">Customized bed file</option>
732 </param>
733
734 <when value="tss">
735 <param type="select" name="further_information" label="Further information: Not required for TSS">
736 <option value="na">Not Required</option>
737 </param>
738 <param name="interval_size" type="select" label="Interval Region Size: Not required for TSS">
739 <option value="na">Not Required</option>
740 </param>
741 <conditional name="flanking_region_option_source_type">
742 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
743 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
744 <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option-->
745 </param>
746 <when value="flanking_region_size">
747 <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
748 </when>
749 <!--when value="flanking_floating_size">
750 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
751 </when-->
752 </conditional>
753 </when>
754 <when value="tes">
755 <param type="select" name="further_information" label="Further information: Not required for TES">
756 <option value="na">Not Required</option>
757 </param>
758 <param name="interval_size" type="select" label="Interval Region Size: Not required for TES">
759 <option value="na">Not Required</option>
760 </param>
761 <conditional name="flanking_region_option_source_type">
762 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
763 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
764 <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option-->
765 </param>
766 <when value="flanking_region_size">
767 <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
768 </when>
769 <!--when value="flanking_floating_size">
770 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
771 </when-->
772 </conditional>
773 </when>
774 <when value="genebody">
775 <param type="select" name="further_information" label="You selected Genebody, further information can be provided for specific regions to plot">
776 <option value="chipseq">ChIP-seq</option>
777 <option value="rnaseq">RNA-seq</option>
778 </param>
779 <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
780 <option value="automatic">Default</option>
781 <option value="0">Small</option>
782 <option value="1">Large</option>
783 </param>
784 <conditional name="flanking_region_option_source_type">
785 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
786 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
787 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
788 </param>
789 <when value="flanking_region_size">
790 <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
791 </when>
792 <when value="flanking_floating_size">
793 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
794 </when>
795 </conditional>
796 </when>
797 <when value="exon">
798 <param type="select" name="further_information" label="You selected Exon, further information can be provided for specific regions to plot">
799 <option value="canonical">Canonical</option>
800 <option value="variant">Variant</option>
801 <option value="promoter">Promoter</option>
802 <option value="polyA">polyA</option>
803 <option value="altAcceptor">altAcceptor</option>
804 <option value="altDonor">altDonor</option>
805 <option value="altBoth">altBoth</option>
806 </param>
807 <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
808 <option value="automatic">Default</option>
809 <option value="0">Small</option>
810 <option value="1">Large</option>
811 </param>
812 <conditional name="flanking_region_option_source_type">
813 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
814 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
815 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
816 </param>
817 <when value="flanking_region_size">
818 <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
819 </when>
820 <when value="flanking_floating_size">
821 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
822 </when>
823 </conditional>
824 </when>
825 <when value="cgi">
826 <param type="select" name="further_information" label="You select CGI, further information can be provided for specific regions to plot">
827 <option value="ProximalPromoter">ProximalPromoter</option>
828 <option value="Genebody">GeneBody</option>
829 <option value="Genedesert">GeneDesert</option>
830 <option value="OtherIntergenic">OtherIntergenic</option>
831 <option value="Pericentromere">Pericentromere</option>
832 <option value="Subtelomere">Subtelomere</option>
833 <option value="Promoter1k">Promoter1k</option>
834 <option value="Promoter3k">Promoter3k</option>
835 </param>
836 <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
837 <option value="automatic">Default</option>
838 <option value="0">Small</option>
839 <option value="1">Large</option>
840 </param>
841 <conditional name="flanking_region_option_source_type">
842 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
843 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
844 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
845 </param>
846 <when value="flanking_region_size">
847 <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
848 </when>
849 <when value="flanking_floating_size">
850 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
851 </when>
852 </conditional>
853 </when>
854 <when value="bed">
855 <param type="select" name="further_information" label="Further information: Not required for bed input">
856 <option value="na">Not Required</option>
857 </param>
858 <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
859 <option value="automatic">Default</option>
860 <option value="0">Small</option>
861 <option value="1">Large</option>
862 </param>
863 <conditional name="flanking_region_option_source_type">
864 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
865 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
866 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
867 </param>
868 <when value="flanking_region_size">
869 <param name="flanking_region_size" size="30" type="text" value="1000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
870 </when>
871 <when value="flanking_floating_size">
872 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
873 </when>
874 </conditional>
875 </when>
876 </conditional>
877
878
879 <conditional name="numsamples">
880 <param type="select" name="numsamples2" label="Number of samples to plot">
881 <option value="1">1</option>
882 <option value="2">2</option>
883 <option value="3">3</option>
884 <option value="4">4</option>
885 <option value="5">5</option>
886 <option value="6">6</option>
887 <option value="7">7</option>
888 <option value="8">8</option>
889 <option value="9">9</option>
890 <option value="10">10</option>
891 </param>
892
893 <when value="1">
894 <conditional name="usepair">
895 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
896 <option value="no">No</option>
897 <option value="yes">Yes</option>
898 </param>
899 <when value="no">
900 <!-- START: 1 sample, no refpairs, entry 1-->
901 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
902 <param type="hidden" name="reffile1" value="na"/>
903 <conditional name="genelist1">
904 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
905 <option value="no">Plot whole genome</option>
906 <option value="yes">Provide restricted gene list</option>
907 </param>
908 <when value="no">
909 <param type="hidden" name="genelist1" value="-1"/>
910 </when>
911 <when value="yes">
912 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
913 </when>
914 </conditional>
915 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
916 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
917 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
918 <!-- END: 1 sample, no refpairs, entry 1-->
919 </when>
920 <when value="yes">
921 <!-- START: 1 sample, yes refpairs, entry 1-->
922 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
923 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
924 <conditional name="genelist1">
925 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
926 <option value="no">Plot whole genome</option>
927 <option value="yes">Provide restricted gene list</option>
928 </param>
929 <when value="no">
930 <param type="hidden" name="genelist1" value="-1"/>
931 </when>
932 <when value="yes">
933 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
934 </when>
935 </conditional>
936 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
937 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
938 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
939 <!-- END: 1 sample, yes refpairs, entry 1-->
940 </when>
941 </conditional>
942 </when>
943 <when value="2">
944 <conditional name="usepair">
945 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
946 <option value="no">No</option>
947 <option value="yes">Yes</option>
948 </param>
949 <when value="no">
950 <!-- START: 2 samples, no refpairs, entry 1-->
951 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
952 <param type="hidden" name="reffile1" value="na"/>
953 <conditional name="genelist1">
954 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
955 <option value="no">Plot whole genome</option>
956 <option value="yes">Provide restricted gene list</option>
957 </param>
958 <when value="no">
959 <param type="hidden" name="genelist1" value="-1"/>
960 </when>
961 <when value="yes">
962 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
963 </when>
964 </conditional>
965 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
966 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
967 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
968 <!-- END: 2 samples, no refpairs, entry 1-->
969 <!-- START: 2 samples, no refpairs, entry 2-->
970 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
971 <param type="hidden" name="reffile2" value="na"/>
972 <conditional name="genelist2">
973 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
974 <option value="no">Plot whole genome</option>
975 <option value="yes">Provide restricted gene list</option>
976 </param>
977 <when value="no">
978 <param type="hidden" name="genelist2" value="-1"/>
979 </when>
980 <when value="yes">
981 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
982 </when>
983 </conditional>
984 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
985 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
986 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
987 <!-- END: 2 samples, no refpairs, entry 2-->
988 </when>
989 <when value="yes">
990 <!-- START: 2 samples, yes refpairs, entry 1-->
991 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
992 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
993 <conditional name="genelist1">
994 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
995 <option value="no">Plot whole genome</option>
996 <option value="yes">Provide restricted gene list</option>
997 </param>
998 <when value="no">
999 <param type="hidden" name="genelist1" value="-1"/>
1000 </when>
1001 <when value="yes">
1002 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1003 </when>
1004 </conditional>
1005 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1006 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1007 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1008 <!-- END: 2 samples, yes refpairs, entry 1-->
1009 <!-- START: 2 samples, yes refpairs, entry 2-->
1010 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1011 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1012 <conditional name="genelist2">
1013 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1014 <option value="no">Plot whole genome</option>
1015 <option value="yes">Provide restricted gene list</option>
1016 </param>
1017 <when value="no">
1018 <param type="hidden" name="genelist2" value="-1"/>
1019 </when>
1020 <when value="yes">
1021 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1022 </when>
1023 </conditional>
1024 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1025 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1026 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1027 <!-- END: 2 samples, yes refpairs, entry 2-->
1028 </when>
1029 </conditional>
1030 </when>
1031 <when value="3">
1032 <conditional name="usepair">
1033 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
1034 <option value="no">No</option>
1035 <option value="yes">Yes</option>
1036 </param>
1037 <when value="no">
1038 <!-- START: 3 samples, no refpairs, entry 1-->
1039 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1040 <param type="hidden" name="reffile1" value="na"/>
1041 <conditional name="genelist1">
1042 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1043 <option value="no">Plot whole genome</option>
1044 <option value="yes">Provide restricted gene list</option>
1045 </param>
1046 <when value="no">
1047 <param type="hidden" name="genelist1" value="-1"/>
1048 </when>
1049 <when value="yes">
1050 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1051 </when>
1052 </conditional>
1053 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1054 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1055 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1056 <!-- END: 3 samples, no refpairs, entry 1-->
1057 <!-- START: 3 samples, no refpairs, entry 2-->
1058 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1059 <param type="hidden" name="reffile2" value="na"/>
1060 <conditional name="genelist2">
1061 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1062 <option value="no">Plot whole genome</option>
1063 <option value="yes">Provide restricted gene list</option>
1064 </param>
1065 <when value="no">
1066 <param type="hidden" name="genelist2" value="-1"/>
1067 </when>
1068 <when value="yes">
1069 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1070 </when>
1071 </conditional>
1072 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1073 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1074 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1075 <!-- END: 3 samples, no refpairs, entry 2-->
1076 <!-- START: 3 samples, no refpairs, entry 3-->
1077 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1078 <param type="hidden" name="reffile3" value="na"/>
1079 <conditional name="genelist3">
1080 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1081 <option value="no">Plot whole genome</option>
1082 <option value="yes">Provide restricted gene list</option>
1083 </param>
1084 <when value="no">
1085 <param type="hidden" name="genelist3" value="-1"/>
1086 </when>
1087 <when value="yes">
1088 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1089 </when>
1090 </conditional>
1091 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1092 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1093 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1094 <!-- END: 3 samples, no refpairs, entry 3-->
1095 </when>
1096 <when value="yes">
1097 <!-- START: 3 samples, yes refpairs, entry 1-->
1098 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1099 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1100 <conditional name="genelist1">
1101 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1102 <option value="no">Plot whole genome</option>
1103 <option value="yes">Provide restricted gene list</option>
1104 </param>
1105 <when value="no">
1106 <param type="hidden" name="genelist1" value="-1"/>
1107 </when>
1108 <when value="yes">
1109 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1110 </when>
1111 </conditional>
1112 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1113 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1114 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1115 <!-- END: 3 samples, yes refpairs, entry 1-->
1116 <!-- START: 3 samples, yes refpairs, entry 2-->
1117 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1118 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1119 <conditional name="genelist2">
1120 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1121 <option value="no">Plot whole genome</option>
1122 <option value="yes">Provide restricted gene list</option>
1123 </param>
1124 <when value="no">
1125 <param type="hidden" name="genelist2" value="-1"/>
1126 </when>
1127 <when value="yes">
1128 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1129 </when>
1130 </conditional>
1131 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1132 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1133 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1134 <!-- END: 3 samples, yes refpairs, entry 2-->
1135 <!-- START: 3 samples, yes refpairs, entry 3-->
1136 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1137 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1138 <conditional name="genelist3">
1139 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1140 <option value="no">Plot whole genome</option>
1141 <option value="yes">Provide restricted gene list</option>
1142 </param>
1143 <when value="no">
1144 <param type="hidden" name="genelist3" value="-1"/>
1145 </when>
1146 <when value="yes">
1147 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1148 </when>
1149 </conditional>
1150 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1151 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1152 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1153 <!-- END: 3 samples, yes refpairs, entry 2-->
1154 </when>
1155 </conditional>
1156 </when>
1157 <when value="4">
1158 <conditional name="usepair">
1159 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
1160 <option value="no">No</option>
1161 <option value="yes">Yes</option>
1162 </param>
1163 <when value="no">
1164 <!-- START: 4 samples, no refpairs, entry 1-->
1165 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1166 <param type="hidden" name="reffile1" value="na"/>
1167 <conditional name="genelist1">
1168 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1169 <option value="no">Plot whole genome</option>
1170 <option value="yes">Provide restricted gene list</option>
1171 </param>
1172 <when value="no">
1173 <param type="hidden" name="genelist1" value="-1"/>
1174 </when>
1175 <when value="yes">
1176 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1177 </when>
1178 </conditional>
1179 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1180 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1181 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1182 <!-- END: 4 samples, no refpairs, entry 1-->
1183 <!-- START: 4 samples, no refpairs, entry 2-->
1184 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1185 <param type="hidden" name="reffile2" value="na"/>
1186 <conditional name="genelist2">
1187 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1188 <option value="no">Plot whole genome</option>
1189 <option value="yes">Provide restricted gene list</option>
1190 </param>
1191 <when value="no">
1192 <param type="hidden" name="genelist2" value="-1"/>
1193 </when>
1194 <when value="yes">
1195 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1196 </when>
1197 </conditional>
1198 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1199 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1200 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1201 <!-- END: 4 samples, no refpairs, entry 2-->
1202 <!-- START: 4 samples, no refpairs, entry 3-->
1203 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1204 <param type="hidden" name="reffile3" value="na"/>
1205 <conditional name="genelist3">
1206 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1207 <option value="no">Plot whole genome</option>
1208 <option value="yes">Provide restricted gene list</option>
1209 </param>
1210 <when value="no">
1211 <param type="hidden" name="genelist3" value="-1"/>
1212 </when>
1213 <when value="yes">
1214 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1215 </when>
1216 </conditional>
1217 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1218 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1219 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1220 <!-- END: 4 samples, no refpairs, entry 3-->
1221 <!-- START: 4 samples, no refpairs, entry 4-->
1222 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1223 <param type="hidden" name="reffile4" value="na"/>
1224 <conditional name="genelist4">
1225 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1226 <option value="no">Plot whole genome</option>
1227 <option value="yes">Provide restricted gene list</option>
1228 </param>
1229 <when value="no">
1230 <param type="hidden" name="genelist4" value="-1"/>
1231 </when>
1232 <when value="yes">
1233 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1234 </when>
1235 </conditional>
1236 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1237 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1238 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1239 <!-- END: 4 samples, no refpairs, entry 4-->
1240 </when>
1241 <when value="yes">
1242 <!-- START: 4 samples, yes refpairs, entry 1-->
1243 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1244 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1245 <conditional name="genelist1">
1246 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1247 <option value="no">Plot whole genome</option>
1248 <option value="yes">Provide restricted gene list</option>
1249 </param>
1250 <when value="no">
1251 <param type="hidden" name="genelist1" value="-1"/>
1252 </when>
1253 <when value="yes">
1254 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1255 </when>
1256 </conditional>
1257 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1258 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1259 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1260 <!-- END: 4 samples, yes refpairs, entry 1-->
1261 <!-- START: 4 samples, yes refpairs, entry 2-->
1262 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1263 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1264 <conditional name="genelist2">
1265 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1266 <option value="no">Plot whole genome</option>
1267 <option value="yes">Provide restricted gene list</option>
1268 </param>
1269 <when value="no">
1270 <param type="hidden" name="genelist2" value="-1"/>
1271 </when>
1272 <when value="yes">
1273 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1274 </when>
1275 </conditional>
1276 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1277 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1278 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1279 <!-- END: 4 samples, yes refpairs, entry 2-->
1280 <!-- START: 4 samples, yes refpairs, entry 3-->
1281 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1282 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1283 <conditional name="genelist3">
1284 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1285 <option value="no">Plot whole genome</option>
1286 <option value="yes">Provide restricted gene list</option>
1287 </param>
1288 <when value="no">
1289 <param type="hidden" name="genelist3" value="-1"/>
1290 </when>
1291 <when value="yes">
1292 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1293 </when>
1294 </conditional>
1295 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1296 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1297 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1298 <!-- END: 4 samples, yes refpairs, entry 3-->
1299 <!-- START: 4 samples, yes refpairs, entry 4-->
1300 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1301 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
1302 <conditional name="genelist4">
1303 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1304 <option value="no">Plot whole genome</option>
1305 <option value="yes">Provide restricted gene list</option>
1306 </param>
1307 <when value="no">
1308 <param type="hidden" name="genelist4" value="-1"/>
1309 </when>
1310 <when value="yes">
1311 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1312 </when>
1313 </conditional>
1314 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1315 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1316 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1317 <!-- END: 4 samples, yes refpairs, entry 4-->
1318 </when>
1319 </conditional>
1320 </when>
1321 <when value="5">
1322 <conditional name="usepair">
1323 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
1324 <option value="no">No</option>
1325 <option value="yes">Yes</option>
1326 </param>
1327 <when value="no">
1328 <!-- START: 5 samples, no refpairs, entry 1-->
1329 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1330 <param type="hidden" name="reffile1" value="na"/>
1331 <conditional name="genelist1">
1332 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1333 <option value="no">Plot whole genome</option>
1334 <option value="yes">Provide restricted gene list</option>
1335 </param>
1336 <when value="no">
1337 <param type="hidden" name="genelist1" value="-1"/>
1338 </when>
1339 <when value="yes">
1340 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1341 </when>
1342 </conditional>
1343 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1344 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1345 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1346 <!-- END: 5 samples, no refpairs, entry 1-->
1347 <!-- START: 5 samples, no refpairs, entry 2-->
1348 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1349 <param type="hidden" name="reffile2" value="na"/>
1350 <conditional name="genelist2">
1351 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1352 <option value="no">Plot whole genome</option>
1353 <option value="yes">Provide restricted gene list</option>
1354 </param>
1355 <when value="no">
1356 <param type="hidden" name="genelist2" value="-1"/>
1357 </when>
1358 <when value="yes">
1359 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1360 </when>
1361 </conditional>
1362 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1363 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1364 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1365 <!-- END: 5 samples, no refpairs, entry 2-->
1366 <!-- START: 5 samples, no refpairs, entry 3-->
1367 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1368 <param type="hidden" name="reffile3" value="na"/>
1369 <conditional name="genelist3">
1370 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1371 <option value="no">Plot whole genome</option>
1372 <option value="yes">Provide restricted gene list</option>
1373 </param>
1374 <when value="no">
1375 <param type="hidden" name="genelist3" value="-1"/>
1376 </when>
1377 <when value="yes">
1378 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1379 </when>
1380 </conditional>
1381 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1382 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1383 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1384 <!-- END: 5 samples, no refpairs, entry 3-->
1385 <!-- START: 5 samples, no refpairs, entry 4-->
1386 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1387 <param type="hidden" name="reffile4" value="na"/>
1388 <conditional name="genelist4">
1389 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1390 <option value="no">Plot whole genome</option>
1391 <option value="yes">Provide restricted gene list</option>
1392 </param>
1393 <when value="no">
1394 <param type="hidden" name="genelist4" value="-1"/>
1395 </when>
1396 <when value="yes">
1397 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1398 </when>
1399 </conditional>
1400 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1401 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1402 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1403 <!-- END: 5 samples, no refpairs, entry 4-->
1404 <!-- START: 5 samples, no refpairs, entry 5-->
1405 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1406 <param type="hidden" name="reffile5" value="na"/>
1407 <conditional name="genelist5">
1408 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1409 <option value="no">Plot whole genome</option>
1410 <option value="yes">Provide restricted gene list</option>
1411 </param>
1412 <when value="no">
1413 <param type="hidden" name="genelist5" value="-1"/>
1414 </when>
1415 <when value="yes">
1416 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1417 </when>
1418 </conditional>
1419 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1420 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1421 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1422 <!-- END: 5 samples, no refpairs, entry 5-->
1423 </when>
1424 <when value="yes">
1425 <!-- START: 5 samples, yes refpairs, entry 1-->
1426 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1427 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1428 <conditional name="genelist1">
1429 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1430 <option value="no">Plot whole genome</option>
1431 <option value="yes">Provide restricted gene list</option>
1432 </param>
1433 <when value="no">
1434 <param type="hidden" name="genelist1" value="-1"/>
1435 </when>
1436 <when value="yes">
1437 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1438 </when>
1439 </conditional>
1440 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1441 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1442 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1443 <!-- END: 5 samples, yes refpairs, entry 1-->
1444 <!-- START: 5 samples, yes refpairs, entry 2-->
1445 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1446 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1447 <conditional name="genelist2">
1448 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1449 <option value="no">Plot whole genome</option>
1450 <option value="yes">Provide restricted gene list</option>
1451 </param>
1452 <when value="no">
1453 <param type="hidden" name="genelist2" value="-1"/>
1454 </when>
1455 <when value="yes">
1456 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1457 </when>
1458 </conditional>
1459 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1460 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1461 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1462 <!-- END: 5 samples, yes refpairs, entry 2-->
1463 <!-- START: 5 samples, yes refpairs, entry 3-->
1464 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1465 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1466 <conditional name="genelist3">
1467 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1468 <option value="no">Plot whole genome</option>
1469 <option value="yes">Provide restricted gene list</option>
1470 </param>
1471 <when value="no">
1472 <param type="hidden" name="genelist3" value="-1"/>
1473 </when>
1474 <when value="yes">
1475 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1476 </when>
1477 </conditional>
1478 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1479 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1480 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1481 <!-- END: 5 samples, yes refpairs, entry 3-->
1482 <!-- START: 5 samples, yes refpairs, entry 4-->
1483 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1484 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
1485 <conditional name="genelist4">
1486 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1487 <option value="no">Plot whole genome</option>
1488 <option value="yes">Provide restricted gene list</option>
1489 </param>
1490 <when value="no">
1491 <param type="hidden" name="genelist4" value="-1"/>
1492 </when>
1493 <when value="yes">
1494 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1495 </when>
1496 </conditional>
1497 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1498 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1499 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1500 <!-- END: 5 samples, yes refpairs, entry 4-->
1501 <!-- START: 5 samples, yes refpairs, entry 5-->
1502 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1503 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
1504 <conditional name="genelist5">
1505 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1506 <option value="no">Plot whole genome</option>
1507 <option value="yes">Provide restricted gene list</option>
1508 </param>
1509 <when value="no">
1510 <param type="hidden" name="genelist5" value="-1"/>
1511 </when>
1512 <when value="yes">
1513 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1514 </when>
1515 </conditional>
1516 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1517 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1518 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1519 <!-- END: 5 samples, yes refpairs, entry 5-->
1520 </when>
1521 </conditional>
1522 </when>
1523 <when value="6">
1524 <conditional name="usepair">
1525 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
1526 <option value="no">No</option>
1527 <option value="yes">Yes</option>
1528 </param>
1529 <when value="no">
1530 <!-- START: 6 samples, no refpairs, entry 1-->
1531 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1532 <param type="hidden" name="reffile1" value="na"/>
1533 <conditional name="genelist1">
1534 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1535 <option value="no">Plot whole genome</option>
1536 <option value="yes">Provide restricted gene list</option>
1537 </param>
1538 <when value="no">
1539 <param type="hidden" name="genelist1" value="-1"/>
1540 </when>
1541 <when value="yes">
1542 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1543 </when>
1544 </conditional>
1545 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1546 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1547 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1548 <!-- END: 6 samples, no refpairs, entry 1-->
1549 <!-- START: 6 samples, no refpairs, entry 2-->
1550 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1551 <param type="hidden" name="reffile2" value="na"/>
1552 <conditional name="genelist2">
1553 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1554 <option value="no">Plot whole genome</option>
1555 <option value="yes">Provide restricted gene list</option>
1556 </param>
1557 <when value="no">
1558 <param type="hidden" name="genelist2" value="-1"/>
1559 </when>
1560 <when value="yes">
1561 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1562 </when>
1563 </conditional>
1564 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1565 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1566 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1567 <!-- END: 6 samples, no refpairs, entry 2-->
1568 <!-- START: 6 samples, no refpairs, entry 3-->
1569 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1570 <param type="hidden" name="reffile3" value="na"/>
1571 <conditional name="genelist3">
1572 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1573 <option value="no">Plot whole genome</option>
1574 <option value="yes">Provide restricted gene list</option>
1575 </param>
1576 <when value="no">
1577 <param type="hidden" name="genelist3" value="-1"/>
1578 </when>
1579 <when value="yes">
1580 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1581 </when>
1582 </conditional>
1583 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1584 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1585 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1586 <!-- END: 6 samples, no refpairs, entry 3-->
1587 <!-- START: 6 samples, no refpairs, entry 4-->
1588 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1589 <param type="hidden" name="reffile4" value="na"/>
1590 <conditional name="genelist4">
1591 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1592 <option value="no">Plot whole genome</option>
1593 <option value="yes">Provide restricted gene list</option>
1594 </param>
1595 <when value="no">
1596 <param type="hidden" name="genelist4" value="-1"/>
1597 </when>
1598 <when value="yes">
1599 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1600 </when>
1601 </conditional>
1602 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1603 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1604 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1605 <!-- END: 6 samples, no refpairs, entry 4-->
1606 <!-- START: 6 samples, no refpairs, entry 5-->
1607 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1608 <param type="hidden" name="reffile5" value="na"/>
1609 <conditional name="genelist5">
1610 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1611 <option value="no">Plot whole genome</option>
1612 <option value="yes">Provide restricted gene list</option>
1613 </param>
1614 <when value="no">
1615 <param type="hidden" name="genelist5" value="-1"/>
1616 </when>
1617 <when value="yes">
1618 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1619 </when>
1620 </conditional>
1621 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1622 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1623 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1624 <!-- END: 6 samples, no refpairs, entry 5-->
1625 <!-- START: 6 samples, no refpairs, entry 6-->
1626 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
1627 <param type="hidden" name="reffile6" value="na"/>
1628 <conditional name="genelist6">
1629 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
1630 <option value="no">Plot whole genome</option>
1631 <option value="yes">Provide restricted gene list</option>
1632 </param>
1633 <when value="no">
1634 <param type="hidden" name="genelist6" value="-1"/>
1635 </when>
1636 <when value="yes">
1637 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
1638 </when>
1639 </conditional>
1640 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
1641 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
1642 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
1643 <!-- END: 6 samples, no refpairs, entry 6-->
1644 </when>
1645 <when value="yes">
1646 <!-- START: 6 samples, yes refpairs, entry 1-->
1647 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1648 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1649 <conditional name="genelist1">
1650 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1651 <option value="no">Plot whole genome</option>
1652 <option value="yes">Provide restricted gene list</option>
1653 </param>
1654 <when value="no">
1655 <param type="hidden" name="genelist1" value="-1"/>
1656 </when>
1657 <when value="yes">
1658 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1659 </when>
1660 </conditional>
1661 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1662 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1663 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1664 <!-- END: 6 samples, yes refpairs, entry 1-->
1665 <!-- START: 6 samples, yes refpairs, entry 2-->
1666 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1667 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1668 <conditional name="genelist2">
1669 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1670 <option value="no">Plot whole genome</option>
1671 <option value="yes">Provide restricted gene list</option>
1672 </param>
1673 <when value="no">
1674 <param type="hidden" name="genelist2" value="-1"/>
1675 </when>
1676 <when value="yes">
1677 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1678 </when>
1679 </conditional>
1680 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1681 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1682 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1683 <!-- END: 6 samples, yes refpairs, entry 2-->
1684 <!-- START: 6 samples, yes refpairs, entry 3-->
1685 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1686 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1687 <conditional name="genelist3">
1688 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1689 <option value="no">Plot whole genome</option>
1690 <option value="yes">Provide restricted gene list</option>
1691 </param>
1692 <when value="no">
1693 <param type="hidden" name="genelist3" value="-1"/>
1694 </when>
1695 <when value="yes">
1696 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1697 </when>
1698 </conditional>
1699 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1700 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1701 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1702 <!-- END: 6 samples, yes refpairs, entry 3-->
1703 <!-- START: 6 samples, yes refpairs, entry 4-->
1704 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1705 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
1706 <conditional name="genelist4">
1707 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1708 <option value="no">Plot whole genome</option>
1709 <option value="yes">Provide restricted gene list</option>
1710 </param>
1711 <when value="no">
1712 <param type="hidden" name="genelist4" value="-1"/>
1713 </when>
1714 <when value="yes">
1715 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1716 </when>
1717 </conditional>
1718 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1719 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1720 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1721 <!-- END: 6 samples, yes refpairs, entry 4-->
1722 <!-- START: 6 samples, yes refpairs, entry 5-->
1723 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1724 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
1725 <conditional name="genelist5">
1726 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1727 <option value="no">Plot whole genome</option>
1728 <option value="yes">Provide restricted gene list</option>
1729 </param>
1730 <when value="no">
1731 <param type="hidden" name="genelist5" value="-1"/>
1732 </when>
1733 <when value="yes">
1734 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1735 </when>
1736 </conditional>
1737 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1738 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1739 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1740 <!-- END: 6 samples, yes refpairs, entry 5-->
1741 <!-- START: 6 samples, yes refpairs, entry 6-->
1742 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
1743 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
1744 <conditional name="genelist6">
1745 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
1746 <option value="no">Plot whole genome</option>
1747 <option value="yes">Provide restricted gene list</option>
1748 </param>
1749 <when value="no">
1750 <param type="hidden" name="genelist6" value="-1"/>
1751 </when>
1752 <when value="yes">
1753 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
1754 </when>
1755 </conditional>
1756 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
1757 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
1758 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
1759 <!-- END: 6 samples, yes refpairs, entry 6-->
1760 </when>
1761 </conditional>
1762 </when>
1763 <when value="7">
1764 <conditional name="usepair">
1765 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
1766 <option value="no">No</option>
1767 <option value="yes">Yes</option>
1768 </param>
1769 <when value="no">
1770 <!-- START: 7 samples, no refpairs, entry 1-->
1771 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1772 <param type="hidden" name="reffile1" value="na"/>
1773 <conditional name="genelist1">
1774 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1775 <option value="no">Plot whole genome</option>
1776 <option value="yes">Provide restricted gene list</option>
1777 </param>
1778 <when value="no">
1779 <param type="hidden" name="genelist1" value="-1"/>
1780 </when>
1781 <when value="yes">
1782 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1783 </when>
1784 </conditional>
1785 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1786 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1787 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1788 <!-- END: 7 samples, no refpairs, entry 1-->
1789 <!-- START: 7 samples, no refpairs, entry 2-->
1790 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1791 <param type="hidden" name="reffile2" value="na"/>
1792 <conditional name="genelist2">
1793 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1794 <option value="no">Plot whole genome</option>
1795 <option value="yes">Provide restricted gene list</option>
1796 </param>
1797 <when value="no">
1798 <param type="hidden" name="genelist2" value="-1"/>
1799 </when>
1800 <when value="yes">
1801 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1802 </when>
1803 </conditional>
1804 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1805 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1806 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1807 <!-- END: 7 samples, no refpairs, entry 2-->
1808 <!-- START: 7 samples, no refpairs, entry 3-->
1809 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1810 <param type="hidden" name="reffile3" value="na"/>
1811 <conditional name="genelist3">
1812 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1813 <option value="no">Plot whole genome</option>
1814 <option value="yes">Provide restricted gene list</option>
1815 </param>
1816 <when value="no">
1817 <param type="hidden" name="genelist3" value="-1"/>
1818 </when>
1819 <when value="yes">
1820 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1821 </when>
1822 </conditional>
1823 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1824 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1825 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1826 <!-- END: 7 samples, no refpairs, entry 3-->
1827 <!-- START: 7 samples, no refpairs, entry 4-->
1828 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1829 <param type="hidden" name="reffile4" value="na"/>
1830 <conditional name="genelist4">
1831 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1832 <option value="no">Plot whole genome</option>
1833 <option value="yes">Provide restricted gene list</option>
1834 </param>
1835 <when value="no">
1836 <param type="hidden" name="genelist4" value="-1"/>
1837 </when>
1838 <when value="yes">
1839 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1840 </when>
1841 </conditional>
1842 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1843 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1844 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1845 <!-- END: 7 samples, no refpairs, entry 4-->
1846 <!-- START: 7 samples, no refpairs, entry 5-->
1847 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1848 <param type="hidden" name="reffile5" value="na"/>
1849 <conditional name="genelist5">
1850 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1851 <option value="no">Plot whole genome</option>
1852 <option value="yes">Provide restricted gene list</option>
1853 </param>
1854 <when value="no">
1855 <param type="hidden" name="genelist5" value="-1"/>
1856 </when>
1857 <when value="yes">
1858 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1859 </when>
1860 </conditional>
1861 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1862 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1863 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1864 <!-- END: 7 samples, no refpairs, entry 5-->
1865 <!-- START: 7 samples, no refpairs, entry 6-->
1866 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
1867 <param type="hidden" name="reffile6" value="na"/>
1868 <conditional name="genelist6">
1869 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
1870 <option value="no">Plot whole genome</option>
1871 <option value="yes">Provide restricted gene list</option>
1872 </param>
1873 <when value="no">
1874 <param type="hidden" name="genelist6" value="-1"/>
1875 </when>
1876 <when value="yes">
1877 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
1878 </when>
1879 </conditional>
1880 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
1881 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
1882 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
1883 <!-- END: 7 samples, no refpairs, entry 6-->
1884 <!-- START: 7 samples, no refpairs, entry 7-->
1885 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
1886 <param type="hidden" name="reffile7" value="na"/>
1887 <conditional name="genelist7">
1888 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
1889 <option value="no">Plot whole genome</option>
1890 <option value="yes">Provide restricted gene list</option>
1891 </param>
1892 <when value="no">
1893 <param type="hidden" name="genelist7" value="-1"/>
1894 </when>
1895 <when value="yes">
1896 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
1897 </when>
1898 </conditional>
1899 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
1900 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
1901 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
1902 <!-- END: 7 samples, no refpairs, entry 7-->
1903 </when>
1904 <when value="yes">
1905 <!-- START: 7 samples, yes refpairs, entry 1-->
1906 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1907 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1908 <conditional name="genelist1">
1909 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1910 <option value="no">Plot whole genome</option>
1911 <option value="yes">Provide restricted gene list</option>
1912 </param>
1913 <when value="no">
1914 <param type="hidden" name="genelist1" value="-1"/>
1915 </when>
1916 <when value="yes">
1917 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1918 </when>
1919 </conditional>
1920 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1921 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1922 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1923 <!-- END: 7 samples, yes refpairs, entry 1-->
1924 <!-- START: 7 samples, yes refpairs, entry 2-->
1925 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1926 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1927 <conditional name="genelist2">
1928 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1929 <option value="no">Plot whole genome</option>
1930 <option value="yes">Provide restricted gene list</option>
1931 </param>
1932 <when value="no">
1933 <param type="hidden" name="genelist2" value="-1"/>
1934 </when>
1935 <when value="yes">
1936 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1937 </when>
1938 </conditional>
1939 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1940 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1941 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1942 <!-- END: 7 samples, yes refpairs, entry 2-->
1943 <!-- START: 7 samples, yes refpairs, entry 3-->
1944 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1945 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1946 <conditional name="genelist3">
1947 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1948 <option value="no">Plot whole genome</option>
1949 <option value="yes">Provide restricted gene list</option>
1950 </param>
1951 <when value="no">
1952 <param type="hidden" name="genelist3" value="-1"/>
1953 </when>
1954 <when value="yes">
1955 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1956 </when>
1957 </conditional>
1958 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1959 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1960 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1961 <!-- END: 7 samples, yes refpairs, entry 3-->
1962 <!-- START: 7 samples, yes refpairs, entry 4-->
1963 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1964 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
1965 <conditional name="genelist4">
1966 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1967 <option value="no">Plot whole genome</option>
1968 <option value="yes">Provide restricted gene list</option>
1969 </param>
1970 <when value="no">
1971 <param type="hidden" name="genelist4" value="-1"/>
1972 </when>
1973 <when value="yes">
1974 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1975 </when>
1976 </conditional>
1977 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1978 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1979 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1980 <!-- END: 7 samples, yes refpairs, entry 4-->
1981 <!-- START: 7 samples, yes refpairs, entry 5-->
1982 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1983 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
1984 <conditional name="genelist5">
1985 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1986 <option value="no">Plot whole genome</option>
1987 <option value="yes">Provide restricted gene list</option>
1988 </param>
1989 <when value="no">
1990 <param type="hidden" name="genelist5" value="-1"/>
1991 </when>
1992 <when value="yes">
1993 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1994 </when>
1995 </conditional>
1996 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1997 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1998 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1999 <!-- END: 7 samples, yes refpairs, entry 5-->
2000 <!-- START: 7 samples, yes refpairs, entry 6-->
2001 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2002 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
2003 <conditional name="genelist6">
2004 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2005 <option value="no">Plot whole genome</option>
2006 <option value="yes">Provide restricted gene list</option>
2007 </param>
2008 <when value="no">
2009 <param type="hidden" name="genelist6" value="-1"/>
2010 </when>
2011 <when value="yes">
2012 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2013 </when>
2014 </conditional>
2015 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2016 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2017 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2018 <!-- END: 7 samples, yes refpairs, entry 6-->
2019 <!-- START: 7 samples, yes refpairs, entry 7-->
2020 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2021 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
2022 <conditional name="genelist7">
2023 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2024 <option value="no">Plot whole genome</option>
2025 <option value="yes">Provide restricted gene list</option>
2026 </param>
2027 <when value="no">
2028 <param type="hidden" name="genelist7" value="-1"/>
2029 </when>
2030 <when value="yes">
2031 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2032 </when>
2033 </conditional>
2034 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2035 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2036 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2037 <!-- END: 7 samples, yes refpairs, entry 7-->
2038 </when>
2039 </conditional>
2040 </when>
2041 <when value="8">
2042 <conditional name="usepair">
2043 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
2044 <option value="no">No</option>
2045 <option value="yes">Yes</option>
2046 </param>
2047 <when value="no">
2048 <!-- START: 8 samples, no refpairs, entry 1-->
2049 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2050 <param type="hidden" name="reffile1" value="na"/>
2051 <conditional name="genelist1">
2052 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2053 <option value="no">Plot whole genome</option>
2054 <option value="yes">Provide restricted gene list</option>
2055 </param>
2056 <when value="no">
2057 <param type="hidden" name="genelist1" value="-1"/>
2058 </when>
2059 <when value="yes">
2060 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2061 </when>
2062 </conditional>
2063 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2064 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2065 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2066 <!-- END: 8 samples, no refpairs, entry 1-->
2067 <!-- START: 8 samples, no refpairs, entry 2-->
2068 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2069 <param type="hidden" name="reffile2" value="na"/>
2070 <conditional name="genelist2">
2071 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2072 <option value="no">Plot whole genome</option>
2073 <option value="yes">Provide restricted gene list</option>
2074 </param>
2075 <when value="no">
2076 <param type="hidden" name="genelist2" value="-1"/>
2077 </when>
2078 <when value="yes">
2079 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2080 </when>
2081 </conditional>
2082 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2083 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2084 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2085 <!-- END: 8 samples, no refpairs, entry 2-->
2086 <!-- START: 8 samples, no refpairs, entry 3-->
2087 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2088 <param type="hidden" name="reffile3" value="na"/>
2089 <conditional name="genelist3">
2090 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2091 <option value="no">Plot whole genome</option>
2092 <option value="yes">Provide restricted gene list</option>
2093 </param>
2094 <when value="no">
2095 <param type="hidden" name="genelist3" value="-1"/>
2096 </when>
2097 <when value="yes">
2098 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2099 </when>
2100 </conditional>
2101 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2102 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2103 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2104 <!-- END: 8 samples, no refpairs, entry 3-->
2105 <!-- START: 8 samples, no refpairs, entry 4-->
2106 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2107 <param type="hidden" name="reffile4" value="na"/>
2108 <conditional name="genelist4">
2109 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2110 <option value="no">Plot whole genome</option>
2111 <option value="yes">Provide restricted gene list</option>
2112 </param>
2113 <when value="no">
2114 <param type="hidden" name="genelist4" value="-1"/>
2115 </when>
2116 <when value="yes">
2117 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2118 </when>
2119 </conditional>
2120 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2121 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2122 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2123 <!-- END: 8 samples, no refpairs, entry 4-->
2124 <!-- START: 8 samples, no refpairs, entry 5-->
2125 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2126 <param type="hidden" name="reffile5" value="na"/>
2127 <conditional name="genelist5">
2128 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2129 <option value="no">Plot whole genome</option>
2130 <option value="yes">Provide restricted gene list</option>
2131 </param>
2132 <when value="no">
2133 <param type="hidden" name="genelist5" value="-1"/>
2134 </when>
2135 <when value="yes">
2136 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2137 </when>
2138 </conditional>
2139 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2140 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2141 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2142 <!-- END: 8 samples, no refpairs, entry 5-->
2143 <!-- START: 8 samples, no refpairs, entry 6-->
2144 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2145 <param type="hidden" name="reffile6" value="na"/>
2146 <conditional name="genelist6">
2147 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2148 <option value="no">Plot whole genome</option>
2149 <option value="yes">Provide restricted gene list</option>
2150 </param>
2151 <when value="no">
2152 <param type="hidden" name="genelist6" value="-1"/>
2153 </when>
2154 <when value="yes">
2155 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2156 </when>
2157 </conditional>
2158 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2159 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2160 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2161 <!-- END: 8 samples, no refpairs, entry 6-->
2162 <!-- START: 8 samples, no refpairs, entry 7-->
2163 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2164 <param type="hidden" name="reffile7" value="na"/>
2165 <conditional name="genelist7">
2166 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2167 <option value="no">Plot whole genome</option>
2168 <option value="yes">Provide restricted gene list</option>
2169 </param>
2170 <when value="no">
2171 <param type="hidden" name="genelist7" value="-1"/>
2172 </when>
2173 <when value="yes">
2174 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2175 </when>
2176 </conditional>
2177 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2178 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2179 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2180 <!-- END: 8 samples, no refpairs, entry 7-->
2181 <!-- START: 8 samples, no refpairs, entry 8-->
2182 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2183 <param type="hidden" name="reffile8" value="na"/>
2184 <conditional name="genelist7">
2185 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2186 <option value="no">Plot whole genome</option>
2187 <option value="yes">Provide restricted gene list</option>
2188 </param>
2189 <when value="no">
2190 <param type="hidden" name="genelist8" value="-1"/>
2191 </when>
2192 <when value="yes">
2193 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2194 </when>
2195 </conditional>
2196 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2197 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2198 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2199 <!-- END: 8 samples, no refpairs, entry 8-->
2200 </when>
2201 <when value="yes">
2202 <!-- START: 8 samples, yes refpairs, entry 1-->
2203 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2204 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
2205 <conditional name="genelist1">
2206 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2207 <option value="no">Plot whole genome</option>
2208 <option value="yes">Provide restricted gene list</option>
2209 </param>
2210 <when value="no">
2211 <param type="hidden" name="genelist1" value="-1"/>
2212 </when>
2213 <when value="yes">
2214 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2215 </when>
2216 </conditional>
2217 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2218 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2219 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2220 <!-- END: 8 samples, yes refpairs, entry 1-->
2221 <!-- START: 8 samples, yes refpairs, entry 2-->
2222 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2223 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
2224 <conditional name="genelist2">
2225 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2226 <option value="no">Plot whole genome</option>
2227 <option value="yes">Provide restricted gene list</option>
2228 </param>
2229 <when value="no">
2230 <param type="hidden" name="genelist2" value="-1"/>
2231 </when>
2232 <when value="yes">
2233 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2234 </when>
2235 </conditional>
2236 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2237 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2238 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2239 <!-- END: 8 samples, yes refpairs, entry 2-->
2240 <!-- START: 8 samples, yes refpairs, entry 3-->
2241 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2242 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
2243 <conditional name="genelist3">
2244 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2245 <option value="no">Plot whole genome</option>
2246 <option value="yes">Provide restricted gene list</option>
2247 </param>
2248 <when value="no">
2249 <param type="hidden" name="genelist3" value="-1"/>
2250 </when>
2251 <when value="yes">
2252 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2253 </when>
2254 </conditional>
2255 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2256 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2257 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2258 <!-- END: 8 samples, yes refpairs, entry 3-->
2259 <!-- START: 8 samples, yes refpairs, entry 4-->
2260 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2261 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
2262 <conditional name="genelist4">
2263 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2264 <option value="no">Plot whole genome</option>
2265 <option value="yes">Provide restricted gene list</option>
2266 </param>
2267 <when value="no">
2268 <param type="hidden" name="genelist4" value="-1"/>
2269 </when>
2270 <when value="yes">
2271 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2272 </when>
2273 </conditional>
2274 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2275 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2276 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2277 <!-- END: 8 samples, yes refpairs, entry 4-->
2278 <!-- START: 8 samples, yes refpairs, entry 5-->
2279 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2280 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
2281 <conditional name="genelist5">
2282 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2283 <option value="no">Plot whole genome</option>
2284 <option value="yes">Provide restricted gene list</option>
2285 </param>
2286 <when value="no">
2287 <param type="hidden" name="genelist5" value="-1"/>
2288 </when>
2289 <when value="yes">
2290 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2291 </when>
2292 </conditional>
2293 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2294 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2295 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2296 <!-- END: 8 samples, yes refpairs, entry 5-->
2297 <!-- START: 8 samples, yes refpairs, entry 6-->
2298 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2299 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
2300 <conditional name="genelist6">
2301 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2302 <option value="no">Plot whole genome</option>
2303 <option value="yes">Provide restricted gene list</option>
2304 </param>
2305 <when value="no">
2306 <param type="hidden" name="genelist6" value="-1"/>
2307 </when>
2308 <when value="yes">
2309 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2310 </when>
2311 </conditional>
2312 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2313 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2314 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2315 <!-- END: 8 samples, yes refpairs, entry 6-->
2316 <!-- START: 8 samples, yes refpairs, entry 7-->
2317 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2318 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
2319 <conditional name="genelist7">
2320 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2321 <option value="no">Plot whole genome</option>
2322 <option value="yes">Provide restricted gene list</option>
2323 </param>
2324 <when value="no">
2325 <param type="hidden" name="genelist7" value="-1"/>
2326 </when>
2327 <when value="yes">
2328 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2329 </when>
2330 </conditional>
2331 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2332 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2333 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2334 <!-- END: 8 samples, yes refpairs, entry 7-->
2335 <!-- START: 8 samples, yes refpairs, entry 8-->
2336 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2337 <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/>
2338 <conditional name="genelist8">
2339 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2340 <option value="no">Plot whole genome</option>
2341 <option value="yes">Provide restricted gene list</option>
2342 </param>
2343 <when value="no">
2344 <param type="hidden" name="genelist8" value="-1"/>
2345 </when>
2346 <when value="yes">
2347 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2348 </when>
2349 </conditional>
2350 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2351 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2352 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2353 <!-- END: 8 samples, yes refpairs, entry 8-->
2354 </when>
2355 </conditional>
2356 </when>
2357 <when value="9">
2358 <conditional name="usepair">
2359 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
2360 <option value="no">No</option>
2361 <option value="yes">Yes</option>
2362 </param>
2363 <when value="no">
2364 <!-- START: 9 samples, no refpairs, entry 1-->
2365 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2366 <param type="hidden" name="reffile1" value="na"/>
2367 <conditional name="genelist1">
2368 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2369 <option value="no">Plot whole genome</option>
2370 <option value="yes">Provide restricted gene list</option>
2371 </param>
2372 <when value="no">
2373 <param type="hidden" name="genelist1" value="-1"/>
2374 </when>
2375 <when value="yes">
2376 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2377 </when>
2378 </conditional>
2379 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2380 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2381 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2382 <!-- END: 9 samples, no refpairs, entry 1-->
2383 <!-- START: 9 samples, no refpairs, entry 2-->
2384 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2385 <param type="hidden" name="reffile2" value="na"/>
2386 <conditional name="genelist2">
2387 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2388 <option value="no">Plot whole genome</option>
2389 <option value="yes">Provide restricted gene list</option>
2390 </param>
2391 <when value="no">
2392 <param type="hidden" name="genelist2" value="-1"/>
2393 </when>
2394 <when value="yes">
2395 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2396 </when>
2397 </conditional>
2398 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2399 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2400 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2401 <!-- END: 9 samples, no refpairs, entry 2-->
2402 <!-- START: 9 samples, no refpairs, entry 3-->
2403 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2404 <param type="hidden" name="reffile3" value="na"/>
2405 <conditional name="genelist3">
2406 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2407 <option value="no">Plot whole genome</option>
2408 <option value="yes">Provide restricted gene list</option>
2409 </param>
2410 <when value="no">
2411 <param type="hidden" name="genelist3" value="-1"/>
2412 </when>
2413 <when value="yes">
2414 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2415 </when>
2416 </conditional>
2417 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2418 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2419 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2420 <!-- END: 9 samples, no refpairs, entry 3-->
2421 <!-- START: 9 samples, no refpairs, entry 4-->
2422 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2423 <param type="hidden" name="reffile4" value="na"/>
2424 <conditional name="genelist4">
2425 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2426 <option value="no">Plot whole genome</option>
2427 <option value="yes">Provide restricted gene list</option>
2428 </param>
2429 <when value="no">
2430 <param type="hidden" name="genelist4" value="-1"/>
2431 </when>
2432 <when value="yes">
2433 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2434 </when>
2435 </conditional>
2436 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2437 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2438 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2439 <!-- END: 9 samples, no refpairs, entry 4-->
2440 <!-- START: 9 samples, no refpairs, entry 5-->
2441 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2442 <param type="hidden" name="reffile5" value="na"/>
2443 <conditional name="genelist5">
2444 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2445 <option value="no">Plot whole genome</option>
2446 <option value="yes">Provide restricted gene list</option>
2447 </param>
2448 <when value="no">
2449 <param type="hidden" name="genelist5" value="-1"/>
2450 </when>
2451 <when value="yes">
2452 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2453 </when>
2454 </conditional>
2455 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2456 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2457 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2458 <!-- END: 9 samples, no refpairs, entry 5-->
2459 <!-- START: 9 samples, no refpairs, entry 6-->
2460 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2461 <param type="hidden" name="reffile6" value="na"/>
2462 <conditional name="genelist6">
2463 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2464 <option value="no">Plot whole genome</option>
2465 <option value="yes">Provide restricted gene list</option>
2466 </param>
2467 <when value="no">
2468 <param type="hidden" name="genelist6" value="-1"/>
2469 </when>
2470 <when value="yes">
2471 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2472 </when>
2473 </conditional>
2474 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2475 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2476 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2477 <!-- END: 9 samples, no refpairs, entry 6-->
2478 <!-- START: 9 samples, no refpairs, entry 7-->
2479 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2480 <param type="hidden" name="reffile7" value="na"/>
2481 <conditional name="genelist7">
2482 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2483 <option value="no">Plot whole genome</option>
2484 <option value="yes">Provide restricted gene list</option>
2485 </param>
2486 <when value="no">
2487 <param type="hidden" name="genelist7" value="-1"/>
2488 </when>
2489 <when value="yes">
2490 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2491 </when>
2492 </conditional>
2493 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2494 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2495 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2496 <!-- END: 9 samples, no refpairs, entry 7-->
2497 <!-- START: 9 samples, no refpairs, entry 8-->
2498 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2499 <param type="hidden" name="reffile8" value="na"/>
2500 <conditional name="genelist8">
2501 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2502 <option value="no">Plot whole genome</option>
2503 <option value="yes">Provide restricted gene list</option>
2504 </param>
2505 <when value="no">
2506 <param type="hidden" name="genelist8" value="-1"/>
2507 </when>
2508 <when value="yes">
2509 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2510 </when>
2511 </conditional>
2512 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2513 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2514 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2515 <!-- END: 9 samples, no refpairs, entry 8-->
2516 <!-- START: 9 samples, no refpairs, entry 9-->
2517 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
2518 <param type="hidden" name="reffile9" value="na"/>
2519 <conditional name="genelist9">
2520 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
2521 <option value="no">Plot whole genome</option>
2522 <option value="yes">Provide restricted gene list</option>
2523 </param>
2524 <when value="no">
2525 <param type="hidden" name="genelist9" value="-1"/>
2526 </when>
2527 <when value="yes">
2528 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
2529 </when>
2530 </conditional>
2531 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
2532 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
2533 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
2534 <!-- END: 9 samples, no refpairs, entry 9-->
2535 </when>
2536 <when value="yes">
2537 <!-- START: 9 samples, yes refpairs, entry 1-->
2538 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2539 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
2540 <conditional name="genelist1">
2541 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2542 <option value="no">Plot whole genome</option>
2543 <option value="yes">Provide restricted gene list</option>
2544 </param>
2545 <when value="no">
2546 <param type="hidden" name="genelist1" value="-1"/>
2547 </when>
2548 <when value="yes">
2549 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2550 </when>
2551 </conditional>
2552 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2553 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2554 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2555 <!-- END: 9 samples, yes refpairs, entry 1-->
2556 <!-- START: 9 samples, yes refpairs, entry 2-->
2557 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2558 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
2559 <conditional name="genelist2">
2560 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2561 <option value="no">Plot whole genome</option>
2562 <option value="yes">Provide restricted gene list</option>
2563 </param>
2564 <when value="no">
2565 <param type="hidden" name="genelist2" value="-1"/>
2566 </when>
2567 <when value="yes">
2568 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2569 </when>
2570 </conditional>
2571 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2572 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2573 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2574 <!-- END: 9 samples, yes refpairs, entry 2-->
2575 <!-- START: 9 samples, yes refpairs, entry 3-->
2576 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2577 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
2578 <conditional name="genelist3">
2579 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2580 <option value="no">Plot whole genome</option>
2581 <option value="yes">Provide restricted gene list</option>
2582 </param>
2583 <when value="no">
2584 <param type="hidden" name="genelist3" value="-1"/>
2585 </when>
2586 <when value="yes">
2587 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2588 </when>
2589 </conditional>
2590 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2591 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2592 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2593 <!-- END: 9 samples, yes refpairs, entry 3-->
2594 <!-- START: 9 samples, yes refpairs, entry 4-->
2595 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2596 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
2597 <conditional name="genelist4">
2598 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2599 <option value="no">Plot whole genome</option>
2600 <option value="yes">Provide restricted gene list</option>
2601 </param>
2602 <when value="no">
2603 <param type="hidden" name="genelist4" value="-1"/>
2604 </when>
2605 <when value="yes">
2606 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2607 </when>
2608 </conditional>
2609 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2610 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2611 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2612 <!-- END: 9 samples, yes refpairs, entry 4-->
2613 <!-- START: 9 samples, yes refpairs, entry 5-->
2614 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2615 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
2616 <conditional name="genelist5">
2617 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2618 <option value="no">Plot whole genome</option>
2619 <option value="yes">Provide restricted gene list</option>
2620 </param>
2621 <when value="no">
2622 <param type="hidden" name="genelist5" value="-1"/>
2623 </when>
2624 <when value="yes">
2625 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2626 </when>
2627 </conditional>
2628 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2629 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2630 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2631 <!-- END: 9 samples, yes refpairs, entry 5-->
2632 <!-- START: 9 samples, yes refpairs, entry 6-->
2633 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2634 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
2635 <conditional name="genelist6">
2636 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2637 <option value="no">Plot whole genome</option>
2638 <option value="yes">Provide restricted gene list</option>
2639 </param>
2640 <when value="no">
2641 <param type="hidden" name="genelist6" value="-1"/>
2642 </when>
2643 <when value="yes">
2644 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2645 </when>
2646 </conditional>
2647 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2648 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2649 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2650 <!-- END: 9 samples, yes refpairs, entry 6-->
2651 <!-- START: 9 samples, yes refpairs, entry 7-->
2652 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2653 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
2654 <conditional name="genelist7">
2655 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2656 <option value="no">Plot whole genome</option>
2657 <option value="yes">Provide restricted gene list</option>
2658 </param>
2659 <when value="no">
2660 <param type="hidden" name="genelist7" value="-1"/>
2661 </when>
2662 <when value="yes">
2663 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2664 </when>
2665 </conditional>
2666 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2667 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2668 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2669 <!-- END: 9 samples, yes refpairs, entry 7-->
2670 <!-- START: 9 samples, yes refpairs, entry 8-->
2671 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2672 <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/>
2673 <conditional name="genelist8">
2674 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2675 <option value="no">Plot whole genome</option>
2676 <option value="yes">Provide restricted gene list</option>
2677 </param>
2678 <when value="no">
2679 <param type="hidden" name="genelist8" value="-1"/>
2680 </when>
2681 <when value="yes">
2682 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2683 </when>
2684 </conditional>
2685 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2686 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2687 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2688 <!-- END: 9 samples, yes refpairs, entry 8-->
2689 <!-- START: 9 samples, yes refpairs, entry 9-->
2690 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
2691 <param type="data" name="reffile9" label="Sample 9: Reference BAM file"/>
2692 <conditional name="genelist9">
2693 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
2694 <option value="no">Plot whole genome</option>
2695 <option value="yes">Provide restricted gene list</option>
2696 </param>
2697 <when value="no">
2698 <param type="hidden" name="genelist9" value="-1"/>
2699 </when>
2700 <when value="yes">
2701 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
2702 </when>
2703 </conditional>
2704 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
2705 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
2706 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
2707 <!-- END: 9 samples, yes refpairs, entry 9-->
2708 </when>
2709 </conditional>
2710 </when>
2711 <when value="10">
2712 <conditional name="usepair">
2713 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
2714 <option value="no">No</option>
2715 <option value="yes">Yes</option>
2716 </param>
2717 <when value="no">
2718 <!-- START: 10 samples, no refpairs, entry 1-->
2719 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2720 <param type="hidden" name="reffile1" value="na"/>
2721 <conditional name="genelist1">
2722 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2723 <option value="no">Plot whole genome</option>
2724 <option value="yes">Provide restricted gene list</option>
2725 </param>
2726 <when value="no">
2727 <param type="hidden" name="genelist1" value="-1"/>
2728 </when>
2729 <when value="yes">
2730 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2731 </when>
2732 </conditional>
2733 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2734 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2735 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2736 <!-- END: 10 samples, no refpairs, entry 1-->
2737 <!-- START: 10 samples, no refpairs, entry 2-->
2738 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2739 <param type="hidden" name="reffile2" value="na"/>
2740 <conditional name="genelist2">
2741 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2742 <option value="no">Plot whole genome</option>
2743 <option value="yes">Provide restricted gene list</option>
2744 </param>
2745 <when value="no">
2746 <param type="hidden" name="genelist2" value="-1"/>
2747 </when>
2748 <when value="yes">
2749 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2750 </when>
2751 </conditional>
2752 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2753 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2754 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2755 <!-- END: 10 samples, no refpairs, entry 2-->
2756 <!-- START: 10 samples, no refpairs, entry 3-->
2757 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2758 <param type="hidden" name="reffile3" value="na"/>
2759 <conditional name="genelist3">
2760 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2761 <option value="no">Plot whole genome</option>
2762 <option value="yes">Provide restricted gene list</option>
2763 </param>
2764 <when value="no">
2765 <param type="hidden" name="genelist3" value="-1"/>
2766 </when>
2767 <when value="yes">
2768 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2769 </when>
2770 </conditional>
2771 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2772 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2773 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2774 <!-- END: 10 samples, no refpairs, entry 3-->
2775 <!-- START: 10 samples, no refpairs, entry 4-->
2776 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2777 <param type="hidden" name="reffile4" value="na"/>
2778 <conditional name="genelist4">
2779 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2780 <option value="no">Plot whole genome</option>
2781 <option value="yes">Provide restricted gene list</option>
2782 </param>
2783 <when value="no">
2784 <param type="hidden" name="genelist4" value="-1"/>
2785 </when>
2786 <when value="yes">
2787 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2788 </when>
2789 </conditional>
2790 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2791 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2792 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2793 <!-- END: 10 samples, no refpairs, entry 4-->
2794 <!-- START: 10 samples, no refpairs, entry 5-->
2795 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2796 <param type="hidden" name="reffile5" value="na"/>
2797 <conditional name="genelist5">
2798 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2799 <option value="no">Plot whole genome</option>
2800 <option value="yes">Provide restricted gene list</option>
2801 </param>
2802 <when value="no">
2803 <param type="hidden" name="genelist5" value="-1"/>
2804 </when>
2805 <when value="yes">
2806 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2807 </when>
2808 </conditional>
2809 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2810 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2811 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2812 <!-- END: 10 samples, no refpairs, entry 5-->
2813 <!-- START: 10 samples, no refpairs, entry 6-->
2814 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2815 <param type="hidden" name="reffile6" value="na"/>
2816 <conditional name="genelist6">
2817 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2818 <option value="no">Plot whole genome</option>
2819 <option value="yes">Provide restricted gene list</option>
2820 </param>
2821 <when value="no">
2822 <param type="hidden" name="genelist6" value="-1"/>
2823 </when>
2824 <when value="yes">
2825 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2826 </when>
2827 </conditional>
2828 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2829 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2830 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2831 <!-- END: 10 samples, no refpairs, entry 6-->
2832 <!-- START: 10 samples, no refpairs, entry 7-->
2833 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2834 <param type="hidden" name="reffile7" value="na"/>
2835 <conditional name="genelist7">
2836 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2837 <option value="no">Plot whole genome</option>
2838 <option value="yes">Provide restricted gene list</option>
2839 </param>
2840 <when value="no">
2841 <param type="hidden" name="genelist7" value="-1"/>
2842 </when>
2843 <when value="yes">
2844 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2845 </when>
2846 </conditional>
2847 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2848 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2849 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2850 <!-- END: 10 samples, no refpairs, entry 7-->
2851 <!-- START: 10 samples, no refpairs, entry 8-->
2852 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2853 <param type="hidden" name="reffile8" value="na"/>
2854 <conditional name="genelist8">
2855 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2856 <option value="no">Plot whole genome</option>
2857 <option value="yes">Provide restricted gene list</option>
2858 </param>
2859 <when value="no">
2860 <param type="hidden" name="genelist8" value="-1"/>
2861 </when>
2862 <when value="yes">
2863 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2864 </when>
2865 </conditional>
2866 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2867 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2868 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2869 <!-- END: 10 samples, no refpairs, entry 8-->
2870 <!-- START: 10 samples, no refpairs, entry 9-->
2871 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
2872 <param type="hidden" name="reffile9" value="na"/>
2873 <conditional name="genelist9">
2874 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
2875 <option value="no">Plot whole genome</option>
2876 <option value="yes">Provide restricted gene list</option>
2877 </param>
2878 <when value="no">
2879 <param type="hidden" name="genelist9" value="-1"/>
2880 </when>
2881 <when value="yes">
2882 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
2883 </when>
2884 </conditional>
2885 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
2886 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
2887 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
2888 <!-- END: 10 samples, no refpairs, entry 9-->
2889 <!-- START: 10 samples, no refpairs, entry 10-->
2890 <param type="data" name="bamfile10" label="Sample 10: Input BAM file"/>
2891 <param type="hidden" name="reffile10" value="na"/>
2892 <conditional name="genelist10">
2893 <param type="select" name="usegenelist10" label="Sample 10: Gene list">
2894 <option value="no">Plot whole genome</option>
2895 <option value="yes">Provide restricted gene list</option>
2896 </param>
2897 <when value="no">
2898 <param type="hidden" name="genelist10" value="-1"/>
2899 </when>
2900 <when value="yes">
2901 <param type="data" name="genelist10" label="Choose the uploaded gene list for plotting"/>
2902 </when>
2903 </conditional>
2904 <param type="text" name="title10" value="plot10" label="Sample 10: Image title"/>
2905 <param type="text" name="fraglen10" value="150" label="Sample 10: Expected fragment length"/>
2906 <param type="text" name="linecol10" value="tan3" label="Sample 10: Line plot color"/>
2907 <!-- END: 10 samples, no refpairs, entry 10-->
2908 </when>
2909 <when value="yes">
2910 <!-- START: 10 samples, yes refpairs, entry 1-->
2911 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2912 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
2913 <conditional name="genelist1">
2914 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2915 <option value="no">Plot whole genome</option>
2916 <option value="yes">Provide restricted gene list</option>
2917 </param>
2918 <when value="no">
2919 <param type="hidden" name="genelist1" value="-1"/>
2920 </when>
2921 <when value="yes">
2922 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2923 </when>
2924 </conditional>
2925 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2926 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2927 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2928 <!-- END: 10 samples, yes refpairs, entry 1-->
2929 <!-- START: 10 samples, yes refpairs, entry 2-->
2930 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2931 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
2932 <conditional name="genelist2">
2933 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2934 <option value="no">Plot whole genome</option>
2935 <option value="yes">Provide restricted gene list</option>
2936 </param>
2937 <when value="no">
2938 <param type="hidden" name="genelist2" value="-1"/>
2939 </when>
2940 <when value="yes">
2941 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2942 </when>
2943 </conditional>
2944 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2945 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2946 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2947 <!-- END: 10 samples, yes refpairs, entry 2-->
2948 <!-- START: 10 samples, yes refpairs, entry 3-->
2949 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2950 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
2951 <conditional name="genelist3">
2952 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2953 <option value="no">Plot whole genome</option>
2954 <option value="yes">Provide restricted gene list</option>
2955 </param>
2956 <when value="no">
2957 <param type="hidden" name="genelist3" value="-1"/>
2958 </when>
2959 <when value="yes">
2960 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2961 </when>
2962 </conditional>
2963 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2964 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2965 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2966 <!-- END: 10 samples, yes refpairs, entry 3-->
2967 <!-- START: 10 samples, yes refpairs, entry 4-->
2968 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2969 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
2970 <conditional name="genelist4">
2971 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2972 <option value="no">Plot whole genome</option>
2973 <option value="yes">Provide restricted gene list</option>
2974 </param>
2975 <when value="no">
2976 <param type="hidden" name="genelist4" value="-1"/>
2977 </when>
2978 <when value="yes">
2979 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2980 </when>
2981 </conditional>
2982 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2983 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2984 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2985 <!-- END: 10 samples, yes refpairs, entry 4-->
2986 <!-- START: 10 samples, yes refpairs, entry 5-->
2987 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2988 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
2989 <conditional name="genelist5">
2990 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2991 <option value="no">Plot whole genome</option>
2992 <option value="yes">Provide restricted gene list</option>
2993 </param>
2994 <when value="no">
2995 <param type="hidden" name="genelist5" value="-1"/>
2996 </when>
2997 <when value="yes">
2998 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2999 </when>
3000 </conditional>
3001 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
3002 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
3003 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
3004 <!-- END: 10 samples, yes refpairs, entry 5-->
3005 <!-- START: 10 samples, yes refpairs, entry 6-->
3006 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
3007 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
3008 <conditional name="genelist6">
3009 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
3010 <option value="no">Plot whole genome</option>
3011 <option value="yes">Provide restricted gene list</option>
3012 </param>
3013 <when value="no">
3014 <param type="hidden" name="genelist6" value="-1"/>
3015 </when>
3016 <when value="yes">
3017 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
3018 </when>
3019 </conditional>
3020 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
3021 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
3022 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
3023 <!-- END: 10 samples, yes refpairs, entry 6-->
3024 <!-- START: 10 samples, yes refpairs, entry 7-->
3025 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
3026 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
3027 <conditional name="genelist7">
3028 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
3029 <option value="no">Plot whole genome</option>
3030 <option value="yes">Provide restricted gene list</option>
3031 </param>
3032 <when value="no">
3033 <param type="hidden" name="genelist7" value="-1"/>
3034 </when>
3035 <when value="yes">
3036 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
3037 </when>
3038 </conditional>
3039 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
3040 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
3041 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
3042 <!-- END: 10 samples, yes refpairs, entry 7-->
3043 <!-- START: 10 samples, yes refpairs, entry 8-->
3044 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
3045 <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/>
3046 <conditional name="genelist8">
3047 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
3048 <option value="no">Plot whole genome</option>
3049 <option value="yes">Provide restricted gene list</option>
3050 </param>
3051 <when value="no">
3052 <param type="hidden" name="genelist8" value="-1"/>
3053 </when>
3054 <when value="yes">
3055 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
3056 </when>
3057 </conditional>
3058 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
3059 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
3060 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
3061 <!-- END: 10 samples, yes refpairs, entry 8-->
3062 <!-- START: 10 samples, yes refpairs, entry 9-->
3063 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
3064 <param type="data" name="reffile9" label="Sample 9: Reference BAM file"/>
3065 <conditional name="genelist9">
3066 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
3067 <option value="no">Plot whole genome</option>
3068 <option value="yes">Provide restricted gene list</option>
3069 </param>
3070 <when value="no">
3071 <param type="hidden" name="genelist9" value="-1"/>
3072 </when>
3073 <when value="yes">
3074 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
3075 </when>
3076 </conditional>
3077 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
3078 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
3079 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
3080 <!-- END: 10 samples, yes refpairs, entry 9-->
3081 <!-- START: 10 samples, yes refpairs, entry 10-->
3082 <param type="data" name="bamfile10" label="Sample 10: Input BAM file"/>
3083 <param type="data" name="reffile10" label="Sample 10: Reference BAM file"/>
3084 <conditional name="genelist10">
3085 <param type="select" name="usegenelist10" label="Sample 10: Gene list">
3086 <option value="no">Plot whole genome</option>
3087 <option value="yes">Provide restricted gene list</option>
3088 </param>
3089 <when value="no">
3090 <param type="hidden" name="genelist10" value="-1"/>
3091 </when>
3092 <when value="yes">
3093 <param type="data" name="genelist10" label="Choose the uploaded gene list for plotting"/>
3094 </when>
3095 </conditional>
3096 <param type="text" name="title10" value="plot10" label="Sample 10: Image title"/>
3097 <param type="text" name="fraglen10" value="150" label="Sample 10: Expected fragment length"/>
3098 <param type="text" name="linecol10" value="tan3" label="Sample 10: Line plot color"/>
3099 <!-- END: 10 samples, yes refpairs, entry 10-->
3100 </when>
3101 </conditional>
3102 </when>
3103 </conditional>
3104
3105
3106
3107 <param type="select" name="gene_database" label="Supported gene database: RefSeq, Ensembl">
3108 <option value="ensembl">Ensembl</option>
3109 <option value="refseq">RefSeq</option>
3110 </param>
3111 <param name="randomly_sample" size="10" type="text" value="1" label="Randomly sample the regions for plotting" help="This will randomly sample a portion of the whole genome or the gene lists. This option can be VERY useful if one just wants to get an overview in shorter time."/>
3112 <conditional name="GO">
3113 <param type="select" name="gene_order" label="Gene order algorithm">
3114 <option value="total">Overall enrichment of the 1st profile</option>
3115 <option value="hc">Hierarchical clustering</option>
3116 <option value="max">Peak value of the 1st profile</option>
3117 <option value="prod">Product of all profiles on the same region</option>
3118 <option value="diff">Difference between the 1st and 2nd profiles</option>
3119 <option value="km">K-means clustering</option>
3120 <option value="none">No ranking algorithm applied. Use order in gene list.</option>
3121 </param>
3122 <when value="km">
3123 <param type="text" name="KNC" value="5" label="K-means: Number of clusters" help=""/>
3124 <param type="text" name="MIT" value="20" label="K-means: Number of iterations" help=""/>
3125 <param type="text" name="NRS" value="30" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
3126 </when>
3127 <when value="total">
3128 <param type="hidden" name="KNC" value="NA" />
3129 <param type="hidden" name="MIT" value="NA" />
3130 <param type="hidden" name="NRS" value="NA" />
3131 </when>
3132 <when value="hc">
3133 <param type="hidden" name="KNC" value="NA" />
3134 <param type="hidden" name="MIT" value="NA" />
3135 <param type="hidden" name="NRS" value="NA" />
3136 </when>
3137 <when value="max">
3138 <param type="hidden" name="KNC" value="NA" />
3139 <param type="hidden" name="MIT" value="NA" />
3140 <param type="hidden" name="NRS" value="NA" />
3141 </when>
3142 <when value="prod">
3143 <param type="hidden" name="KNC" value="NA" />
3144 <param type="hidden" name="MIT" value="NA" />
3145 <param type="hidden" name="NRS" value="NA" />
3146 </when>
3147 <when value="diff">
3148 <param type="hidden" name="KNC" value="NA" />
3149 <param type="hidden" name="MIT" value="NA" />
3150 <param type="hidden" name="NRS" value="NA" />
3151 </when>
3152 <when value="none">
3153 <param type="hidden" name="KNC" value="NA" />
3154 <param type="hidden" name="MIT" value="NA" />
3155 <param type="hidden" name="NRS" value="NA" />
3156 </when>
3157 </conditional>
3158 <param name="chunk_size" size="10" type="text" value="100" label="Chunk size for loading genes in batch" help="This parameter controls the behavior of coverage calculation. A smaller value implies lower memory footprint but may increase processing time."/>
3159 <param name="quality_requirement" size="10" type="text" value="20" label="Mapping quality requirement" help="This is the Phred-scale mapping quality score. A score of 20 means an error rate of 1%."/>
3160 <param type="select" name="standard_error" label="Plot standard errors" help="Standard errors will be rendered as shaded area around each curve.">
3161 <option value="1">Yes</option>
3162 <option value="0">No</option>
3163 </param>
3164
3165 <param name="radius_size" size="10" type="text" value="0" label="Fraction of extreme values to be trimmed on both ends" help="The fraction of extreme values that will be trimmed on both ends. Eg. 0.05 will remove 5% of extreme values."/>
3166 <param name="flooding_fraction" size="10" type="text" value="0.02" label="Heatmap flooding fraction" help="Default of 0.02 means that the minimum value is truncated at 2% and the maximum value is truncated at 98%. A higher fraction results in plots that have higher brightness but are less dynamic."/>
3167 <param type="select" name="smooth_method" label="Moving window width to smooth avg. profiles">
3168 <option value="1">No</option>
3169 <option value="3">Slightly</option>
3170 <option value="5">Somewhat</option>
3171 <option value="9">Quite</option>
3172 <option value="13">Super</option>
3173 </param>
3174 <param name="shaded_area" size="10" type="text" value="0" label="Opacity of shaded area under curve" help="Suggested value between 0 and 0.5."/>
3175 <!--
3176 -->
3177 </inputs>
3178
3179 <help></help>
3180 <outputs>
3181 <data format="pdf" name="out_avg_png" />
3182 <data format="pdf" name="out_hm_png" />
3183 <data format="zip" name="out_zip"/>
3184 </outputs>
3185 </tool>