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comparison ngsplot_galaxytoolshed_v1.0/ngsplot_main/ngsplot.xml @ 2:b2d5006b82b8 draft

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author ngsplot
date Wed, 18 Mar 2015 15:43:54 -0400
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children 5621523bbe56
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1:795270a5555c 2:b2d5006b82b8
1 <tool id="ngs.plot" name="ngs.plot">
2
3 <requirements>
4 <requirement type="package" version="2.47.1">ngsplot</requirement>
5 </requirements>
6
7 <command interpreter="perl">
8 #if $numsamples.numsamples2 == "1":
9 runNGSplot.pl
10 $genome_name
11 $genomic_region_source_type.genomic_region
12 $genomic_region_source_type.further_information
13 $genomic_region_source_type.interval_size
14 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
15 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
16 $numsamples.numsamples2
17 $numsamples.usepair.usepair1
18
19 $numsamples.usepair.bamfile1
20 $numsamples.usepair.reffile1
21 $numsamples.usepair.genelist1.usegenelist1
22 $numsamples.usepair.genelist1.genelist1
23 $numsamples.usepair.title1
24 $numsamples.usepair.fraglen1
25 $numsamples.usepair.linecol1
26
27 $gene_database
28 $randomly_sample
29 $GO.gene_order
30 $GO.KNC
31 $GO.MIT
32 $GO.NRS
33 $chunk_size
34 $quality_requirement
35 $standard_error
36 $radius_size
37 $flooding_fraction
38 $smooth_method
39 $shaded_area
40 $out_zip $out_avg_png $out_hm_png
41
42 #else if $numsamples.numsamples2 == "2":
43 runNGSplot.pl
44 $genome_name
45 $genomic_region_source_type.genomic_region
46 $genomic_region_source_type.further_information
47 $genomic_region_source_type.interval_size
48 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
49 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
50 $numsamples.numsamples2
51 $numsamples.usepair.usepair1
52
53 $numsamples.usepair.bamfile1
54 $numsamples.usepair.reffile1
55 $numsamples.usepair.genelist1.usegenelist1
56 $numsamples.usepair.genelist1.genelist1
57 $numsamples.usepair.title1
58 $numsamples.usepair.fraglen1
59 $numsamples.usepair.linecol1
60
61 $numsamples.usepair.bamfile2
62 $numsamples.usepair.reffile2
63 $numsamples.usepair.genelist2.usegenelist2
64 $numsamples.usepair.genelist2.genelist2
65 $numsamples.usepair.title2
66 $numsamples.usepair.fraglen2
67 $numsamples.usepair.linecol2
68
69 $gene_database
70 $randomly_sample
71 $GO.gene_order
72 $GO.KNC
73 $GO.MIT
74 $GO.NRS
75 $chunk_size
76 $quality_requirement
77 $standard_error
78 $radius_size
79 $flooding_fraction
80 $smooth_method
81 $shaded_area
82 $out_zip $out_avg_png $out_hm_png
83
84 #else if $numsamples.numsamples2 == "3":
85 runNGSplot.pl
86 $genome_name
87 $genomic_region_source_type.genomic_region
88 $genomic_region_source_type.further_information
89 $genomic_region_source_type.interval_size
90 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
91 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
92 $numsamples.numsamples2
93 $numsamples.usepair.usepair1
94
95 $numsamples.usepair.bamfile1
96 $numsamples.usepair.reffile1
97 $numsamples.usepair.genelist1.usegenelist1
98 $numsamples.usepair.genelist1.genelist1
99 $numsamples.usepair.title1
100 $numsamples.usepair.fraglen1
101 $numsamples.usepair.linecol1
102
103 $numsamples.usepair.bamfile2
104 $numsamples.usepair.reffile2
105 $numsamples.usepair.genelist2.usegenelist2
106 $numsamples.usepair.genelist2.genelist2
107 $numsamples.usepair.title2
108 $numsamples.usepair.fraglen2
109 $numsamples.usepair.linecol2
110
111 $numsamples.usepair.bamfile3
112 $numsamples.usepair.reffile3
113 $numsamples.usepair.genelist3.usegenelist3
114 $numsamples.usepair.genelist3.genelist3
115 $numsamples.usepair.title3
116 $numsamples.usepair.fraglen3
117 $numsamples.usepair.linecol3
118
119 $gene_database
120 $randomly_sample
121 $GO.gene_order
122 $GO.KNC
123 $GO.MIT
124 $GO.NRS
125 $chunk_size
126 $quality_requirement
127 $standard_error
128 $radius_size
129 $flooding_fraction
130 $smooth_method
131 $shaded_area
132 $out_zip $out_avg_png $out_hm_png
133
134 #else if $numsamples.numsamples2 == "4":
135 runNGSplot.pl
136 $genome_name
137 $genomic_region_source_type.genomic_region
138 $genomic_region_source_type.further_information
139 $genomic_region_source_type.interval_size
140 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
141 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
142 $numsamples.numsamples2
143 $numsamples.usepair.usepair1
144
145 $numsamples.usepair.bamfile1
146 $numsamples.usepair.reffile1
147 $numsamples.usepair.genelist1.usegenelist1
148 $numsamples.usepair.genelist1.genelist1
149 $numsamples.usepair.title1
150 $numsamples.usepair.fraglen1
151 $numsamples.usepair.linecol1
152
153 $numsamples.usepair.bamfile2
154 $numsamples.usepair.reffile2
155 $numsamples.usepair.genelist2.usegenelist2
156 $numsamples.usepair.genelist2.genelist2
157 $numsamples.usepair.title2
158 $numsamples.usepair.fraglen2
159 $numsamples.usepair.linecol2
160
161 $numsamples.usepair.bamfile3
162 $numsamples.usepair.reffile3
163 $numsamples.usepair.genelist3.usegenelist3
164 $numsamples.usepair.genelist3.genelist3
165 $numsamples.usepair.title3
166 $numsamples.usepair.fraglen3
167 $numsamples.usepair.linecol3
168
169 $numsamples.usepair.bamfile4
170 $numsamples.usepair.reffile4
171 $numsamples.usepair.genelist4.usegenelist4
172 $numsamples.usepair.genelist4.genelist4
173 $numsamples.usepair.title4
174 $numsamples.usepair.fraglen4
175 $numsamples.usepair.linecol4
176
177 $gene_database
178 $randomly_sample
179 $GO.gene_order
180 $GO.KNC
181 $GO.MIT
182 $GO.NRS
183 $chunk_size
184 $quality_requirement
185 $standard_error
186 $radius_size
187 $flooding_fraction
188 $smooth_method
189 $shaded_area
190 $out_zip $out_avg_png $out_hm_png
191
192 #else if $numsamples.numsamples2 == "5":
193 runNGSplot.pl
194 $genome_name
195 $genomic_region_source_type.genomic_region
196 $genomic_region_source_type.further_information
197 $genomic_region_source_type.interval_size
198 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
199 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
200 $numsamples.numsamples2
201 $numsamples.usepair.usepair1
202
203 $numsamples.usepair.bamfile1
204 $numsamples.usepair.reffile1
205 $numsamples.usepair.genelist1.usegenelist1
206 $numsamples.usepair.genelist1.genelist1
207 $numsamples.usepair.title1
208 $numsamples.usepair.fraglen1
209 $numsamples.usepair.linecol1
210
211 $numsamples.usepair.bamfile2
212 $numsamples.usepair.reffile2
213 $numsamples.usepair.genelist2.usegenelist2
214 $numsamples.usepair.genelist2.genelist2
215 $numsamples.usepair.title2
216 $numsamples.usepair.fraglen2
217 $numsamples.usepair.linecol2
218
219 $numsamples.usepair.bamfile3
220 $numsamples.usepair.reffile3
221 $numsamples.usepair.genelist3.usegenelist3
222 $numsamples.usepair.genelist3.genelist3
223 $numsamples.usepair.title3
224 $numsamples.usepair.fraglen3
225 $numsamples.usepair.linecol3
226
227 $numsamples.usepair.bamfile4
228 $numsamples.usepair.reffile4
229 $numsamples.usepair.genelist4.usegenelist4
230 $numsamples.usepair.genelist4.genelist4
231 $numsamples.usepair.title4
232 $numsamples.usepair.fraglen4
233 $numsamples.usepair.linecol4
234
235 $numsamples.usepair.bamfile5
236 $numsamples.usepair.reffile5
237 $numsamples.usepair.genelist5.usegenelist5
238 $numsamples.usepair.genelist5.genelist5
239 $numsamples.usepair.title5
240 $numsamples.usepair.fraglen5
241 $numsamples.usepair.linecol5
242
243 $gene_database
244 $randomly_sample
245 $GO.gene_order
246 $GO.KNC
247 $GO.MIT
248 $GO.NRS
249 $chunk_size
250 $quality_requirement
251 $standard_error
252 $radius_size
253 $flooding_fraction
254 $smooth_method
255 $shaded_area
256 $out_zip $out_avg_png $out_hm_png
257
258 #else if $numsamples.numsamples2 == "6":
259 runNGSplot.pl
260 $genome_name
261 $genomic_region_source_type.genomic_region
262 $genomic_region_source_type.further_information
263 $genomic_region_source_type.interval_size
264 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
265 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
266 $numsamples.numsamples2
267 $numsamples.usepair.usepair1
268
269 $numsamples.usepair.bamfile1
270 $numsamples.usepair.reffile1
271 $numsamples.usepair.genelist1.usegenelist1
272 $numsamples.usepair.genelist1.genelist1
273 $numsamples.usepair.title1
274 $numsamples.usepair.fraglen1
275 $numsamples.usepair.linecol1
276
277 $numsamples.usepair.bamfile2
278 $numsamples.usepair.reffile2
279 $numsamples.usepair.genelist2.usegenelist2
280 $numsamples.usepair.genelist2.genelist2
281 $numsamples.usepair.title2
282 $numsamples.usepair.fraglen2
283 $numsamples.usepair.linecol2
284
285 $numsamples.usepair.bamfile3
286 $numsamples.usepair.reffile3
287 $numsamples.usepair.genelist3.usegenelist3
288 $numsamples.usepair.genelist3.genelist3
289 $numsamples.usepair.title3
290 $numsamples.usepair.fraglen3
291 $numsamples.usepair.linecol3
292
293 $numsamples.usepair.bamfile4
294 $numsamples.usepair.reffile4
295 $numsamples.usepair.genelist4.usegenelist4
296 $numsamples.usepair.genelist4.genelist4
297 $numsamples.usepair.title4
298 $numsamples.usepair.fraglen4
299 $numsamples.usepair.linecol4
300
301 $numsamples.usepair.bamfile5
302 $numsamples.usepair.reffile5
303 $numsamples.usepair.genelist5.usegenelist5
304 $numsamples.usepair.genelist5.genelist5
305 $numsamples.usepair.title5
306 $numsamples.usepair.fraglen5
307 $numsamples.usepair.linecol5
308
309 $numsamples.usepair.bamfile6
310 $numsamples.usepair.reffile6
311 $numsamples.usepair.genelist6.usegenelist6
312 $numsamples.usepair.genelist6.genelist6
313 $numsamples.usepair.title6
314 $numsamples.usepair.fraglen6
315 $numsamples.usepair.linecol6
316
317 $gene_database
318 $randomly_sample
319 $GO.gene_order
320 $GO.KNC
321 $GO.MIT
322 $GO.NRS
323 $chunk_size
324 $quality_requirement
325 $standard_error
326 $radius_size
327 $flooding_fraction
328 $smooth_method
329 $shaded_area
330 $out_zip $out_avg_png $out_hm_png
331
332 #else if $numsamples.numsamples2 == "7":
333 runNGSplot.pl
334 $genome_name
335 $genomic_region_source_type.genomic_region
336 $genomic_region_source_type.further_information
337 $genomic_region_source_type.interval_size
338 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
339 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
340 $numsamples.numsamples2
341 $numsamples.usepair.usepair1
342
343 $numsamples.usepair.bamfile1
344 $numsamples.usepair.reffile1
345 $numsamples.usepair.genelist1.usegenelist1
346 $numsamples.usepair.genelist1.genelist1
347 $numsamples.usepair.title1
348 $numsamples.usepair.fraglen1
349 $numsamples.usepair.linecol1
350
351 $numsamples.usepair.bamfile2
352 $numsamples.usepair.reffile2
353 $numsamples.usepair.genelist2.usegenelist2
354 $numsamples.usepair.genelist2.genelist2
355 $numsamples.usepair.title2
356 $numsamples.usepair.fraglen2
357 $numsamples.usepair.linecol2
358
359 $numsamples.usepair.bamfile3
360 $numsamples.usepair.reffile3
361 $numsamples.usepair.genelist3.usegenelist3
362 $numsamples.usepair.genelist3.genelist3
363 $numsamples.usepair.title3
364 $numsamples.usepair.fraglen3
365 $numsamples.usepair.linecol3
366
367 $numsamples.usepair.bamfile4
368 $numsamples.usepair.reffile4
369 $numsamples.usepair.genelist4.usegenelist4
370 $numsamples.usepair.genelist4.genelist4
371 $numsamples.usepair.title4
372 $numsamples.usepair.fraglen4
373 $numsamples.usepair.linecol4
374
375 $numsamples.usepair.bamfile5
376 $numsamples.usepair.reffile5
377 $numsamples.usepair.genelist5.usegenelist5
378 $numsamples.usepair.genelist5.genelist5
379 $numsamples.usepair.title5
380 $numsamples.usepair.fraglen5
381 $numsamples.usepair.linecol5
382
383 $numsamples.usepair.bamfile6
384 $numsamples.usepair.reffile6
385 $numsamples.usepair.genelist6.usegenelist6
386 $numsamples.usepair.genelist6.genelist6
387 $numsamples.usepair.title6
388 $numsamples.usepair.fraglen6
389 $numsamples.usepair.linecol6
390
391 $numsamples.usepair.bamfile7
392 $numsamples.usepair.reffile7
393 $numsamples.usepair.genelist7.usegenelist7
394 $numsamples.usepair.genelist7.genelist7
395 $numsamples.usepair.title7
396 $numsamples.usepair.fraglen7
397 $numsamples.usepair.linecol7
398
399 $gene_database
400 $randomly_sample
401 $GO.gene_order
402 $GO.KNC
403 $GO.MIT
404 $GO.NRS
405 $chunk_size
406 $quality_requirement
407 $standard_error
408 $radius_size
409 $flooding_fraction
410 $smooth_method
411 $shaded_area
412 $out_zip $out_avg_png $out_hm_png
413
414 #else if $numsamples.numsamples2 == "8":
415 runNGSplot.pl
416 $genome_name
417 $genomic_region_source_type.genomic_region
418 $genomic_region_source_type.further_information
419 $genomic_region_source_type.interval_size
420 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
421 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
422 $numsamples.numsamples2
423 $numsamples.usepair.usepair1
424
425 $numsamples.usepair.bamfile1
426 $numsamples.usepair.reffile1
427 $numsamples.usepair.genelist1.usegenelist1
428 $numsamples.usepair.genelist1.genelist1
429 $numsamples.usepair.title1
430 $numsamples.usepair.fraglen1
431 $numsamples.usepair.linecol1
432
433 $numsamples.usepair.bamfile2
434 $numsamples.usepair.reffile2
435 $numsamples.usepair.genelist2.usegenelist2
436 $numsamples.usepair.genelist2.genelist2
437 $numsamples.usepair.title2
438 $numsamples.usepair.fraglen2
439 $numsamples.usepair.linecol2
440
441 $numsamples.usepair.bamfile3
442 $numsamples.usepair.reffile3
443 $numsamples.usepair.genelist3.usegenelist3
444 $numsamples.usepair.genelist3.genelist3
445 $numsamples.usepair.title3
446 $numsamples.usepair.fraglen3
447 $numsamples.usepair.linecol3
448
449 $numsamples.usepair.bamfile4
450 $numsamples.usepair.reffile4
451 $numsamples.usepair.genelist4.usegenelist4
452 $numsamples.usepair.genelist4.genelist4
453 $numsamples.usepair.title4
454 $numsamples.usepair.fraglen4
455 $numsamples.usepair.linecol4
456
457 $numsamples.usepair.bamfile5
458 $numsamples.usepair.reffile5
459 $numsamples.usepair.genelist5.usegenelist5
460 $numsamples.usepair.genelist5.genelist5
461 $numsamples.usepair.title5
462 $numsamples.usepair.fraglen5
463 $numsamples.usepair.linecol5
464
465 $numsamples.usepair.bamfile6
466 $numsamples.usepair.reffile6
467 $numsamples.usepair.genelist6.usegenelist6
468 $numsamples.usepair.genelist6.genelist6
469 $numsamples.usepair.title6
470 $numsamples.usepair.fraglen6
471 $numsamples.usepair.linecol6
472
473 $numsamples.usepair.bamfile7
474 $numsamples.usepair.reffile7
475 $numsamples.usepair.genelist7.usegenelist7
476 $numsamples.usepair.genelist7.genelist7
477 $numsamples.usepair.title7
478 $numsamples.usepair.fraglen7
479 $numsamples.usepair.linecol7
480
481 $numsamples.usepair.bamfile8
482 $numsamples.usepair.reffile8
483 $numsamples.usepair.genelist8.usegenelist8
484 $numsamples.usepair.genelist8.genelist8
485 $numsamples.usepair.title8
486 $numsamples.usepair.fraglen8
487 $numsamples.usepair.linecol8
488
489 $gene_database
490 $randomly_sample
491 $GO.gene_order
492 $GO.KNC
493 $GO.MIT
494 $GO.NRS
495 $chunk_size
496 $quality_requirement
497 $standard_error
498 $radius_size
499 $flooding_fraction
500 $smooth_method
501 $shaded_area
502 $out_zip $out_avg_png $out_hm_png
503
504 #else if $numsamples.numsamples2 == "9":
505 runNGSplot.pl
506 $genome_name
507 $genomic_region_source_type.genomic_region
508 $genomic_region_source_type.further_information
509 $genomic_region_source_type.interval_size
510 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
511 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
512 $numsamples.numsamples2
513 $numsamples.usepair.usepair1
514
515 $numsamples.usepair.bamfile1
516 $numsamples.usepair.reffile1
517 $numsamples.usepair.genelist1.usegenelist1
518 $numsamples.usepair.genelist1.genelist1
519 $numsamples.usepair.title1
520 $numsamples.usepair.fraglen1
521 $numsamples.usepair.linecol1
522
523 $numsamples.usepair.bamfile2
524 $numsamples.usepair.reffile2
525 $numsamples.usepair.genelist2.usegenelist2
526 $numsamples.usepair.genelist2.genelist2
527 $numsamples.usepair.title2
528 $numsamples.usepair.fraglen2
529 $numsamples.usepair.linecol2
530
531 $numsamples.usepair.bamfile3
532 $numsamples.usepair.reffile3
533 $numsamples.usepair.genelist3.usegenelist3
534 $numsamples.usepair.genelist3.genelist3
535 $numsamples.usepair.title3
536 $numsamples.usepair.fraglen3
537 $numsamples.usepair.linecol3
538
539 $numsamples.usepair.bamfile4
540 $numsamples.usepair.reffile4
541 $numsamples.usepair.genelist4.usegenelist4
542 $numsamples.usepair.genelist4.genelist4
543 $numsamples.usepair.title4
544 $numsamples.usepair.fraglen4
545 $numsamples.usepair.linecol4
546
547 $numsamples.usepair.bamfile5
548 $numsamples.usepair.reffile5
549 $numsamples.usepair.genelist5.usegenelist5
550 $numsamples.usepair.genelist5.genelist5
551 $numsamples.usepair.title5
552 $numsamples.usepair.fraglen5
553 $numsamples.usepair.linecol5
554
555 $numsamples.usepair.bamfile6
556 $numsamples.usepair.reffile6
557 $numsamples.usepair.genelist6.usegenelist6
558 $numsamples.usepair.genelist6.genelist6
559 $numsamples.usepair.title6
560 $numsamples.usepair.fraglen6
561 $numsamples.usepair.linecol6
562
563 $numsamples.usepair.bamfile7
564 $numsamples.usepair.reffile7
565 $numsamples.usepair.genelist7.usegenelist7
566 $numsamples.usepair.genelist7.genelist7
567 $numsamples.usepair.title7
568 $numsamples.usepair.fraglen7
569 $numsamples.usepair.linecol7
570
571 $numsamples.usepair.bamfile8
572 $numsamples.usepair.reffile8
573 $numsamples.usepair.genelist8.usegenelist8
574 $numsamples.usepair.genelist8.genelist8
575 $numsamples.usepair.title8
576 $numsamples.usepair.fraglen8
577 $numsamples.usepair.linecol8
578
579 $numsamples.usepair.bamfile9
580 $numsamples.usepair.reffile9
581 $numsamples.usepair.genelist9.usegenelist9
582 $numsamples.usepair.genelist9.genelist9
583 $numsamples.usepair.title9
584 $numsamples.usepair.fraglen9
585 $numsamples.usepair.linecol9
586
587 $gene_database
588 $randomly_sample
589 $GO.gene_order
590 $GO.KNC
591 $GO.MIT
592 $GO.NRS
593 $chunk_size
594 $quality_requirement
595 $standard_error
596 $radius_size
597 $flooding_fraction
598 $smooth_method
599 $shaded_area
600 $out_zip $out_avg_png $out_hm_png
601
602 #else if $numsamples.numsamples2 == "10":
603 runNGSplot.pl
604 $genome_name
605 $genomic_region_source_type.genomic_region
606 $genomic_region_source_type.further_information
607 $genomic_region_source_type.interval_size
608 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
609 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
610 $numsamples.numsamples2
611 $numsamples.usepair.usepair1
612
613 $numsamples.usepair.bamfile1
614 $numsamples.usepair.reffile1
615 $numsamples.usepair.genelist1.usegenelist1
616 $numsamples.usepair.genelist1.genelist1
617 $numsamples.usepair.title1
618 $numsamples.usepair.fraglen1
619 $numsamples.usepair.linecol1
620
621 $numsamples.usepair.bamfile2
622 $numsamples.usepair.reffile2
623 $numsamples.usepair.genelist2.usegenelist2
624 $numsamples.usepair.genelist2.genelist2
625 $numsamples.usepair.title2
626 $numsamples.usepair.fraglen2
627 $numsamples.usepair.linecol2
628
629 $numsamples.usepair.bamfile3
630 $numsamples.usepair.reffile3
631 $numsamples.usepair.genelist3.usegenelist3
632 $numsamples.usepair.genelist3.genelist3
633 $numsamples.usepair.title3
634 $numsamples.usepair.fraglen3
635 $numsamples.usepair.linecol3
636
637 $numsamples.usepair.bamfile4
638 $numsamples.usepair.reffile4
639 $numsamples.usepair.genelist4.usegenelist4
640 $numsamples.usepair.genelist4.genelist4
641 $numsamples.usepair.title4
642 $numsamples.usepair.fraglen4
643 $numsamples.usepair.linecol4
644
645 $numsamples.usepair.bamfile5
646 $numsamples.usepair.reffile5
647 $numsamples.usepair.genelist5.usegenelist5
648 $numsamples.usepair.genelist5.genelist5
649 $numsamples.usepair.title5
650 $numsamples.usepair.fraglen5
651 $numsamples.usepair.linecol5
652
653 $numsamples.usepair.bamfile6
654 $numsamples.usepair.reffile6
655 $numsamples.usepair.genelist6.usegenelist6
656 $numsamples.usepair.genelist6.genelist6
657 $numsamples.usepair.title6
658 $numsamples.usepair.fraglen6
659 $numsamples.usepair.linecol6
660
661 $numsamples.usepair.bamfile7
662 $numsamples.usepair.reffile7
663 $numsamples.usepair.genelist7.usegenelist7
664 $numsamples.usepair.genelist7.genelist7
665 $numsamples.usepair.title7
666 $numsamples.usepair.fraglen7
667 $numsamples.usepair.linecol7
668
669 $numsamples.usepair.bamfile8
670 $numsamples.usepair.reffile8
671 $numsamples.usepair.genelist8.usegenelist8
672 $numsamples.usepair.genelist8.genelist8
673 $numsamples.usepair.title8
674 $numsamples.usepair.fraglen8
675 $numsamples.usepair.linecol8
676
677 $numsamples.usepair.bamfile9
678 $numsamples.usepair.reffile9
679 $numsamples.usepair.genelist9.usegenelist9
680 $numsamples.usepair.genelist9.genelist9
681 $numsamples.usepair.title9
682 $numsamples.usepair.fraglen9
683 $numsamples.usepair.linecol9
684
685 $numsamples.usepair.bamfile10
686 $numsamples.usepair.reffile10
687 $numsamples.usepair.genelist10.usegenelist10
688 $numsamples.usepair.genelist10.genelist10
689 $numsamples.usepair.title10
690 $numsamples.usepair.fraglen10
691 $numsamples.usepair.linecol10
692
693 $gene_database
694 $randomly_sample
695 $GO.gene_order
696 $GO.KNC
697 $GO.MIT
698 $GO.NRS
699 $chunk_size
700 $quality_requirement
701 $standard_error
702 $radius_size
703 $flooding_fraction
704 $smooth_method
705 $shaded_area
706 $out_zip $out_avg_png $out_hm_png
707
708 #end if:
709
710 </command>
711
712 <!-->
713 <-->
714
715 <inputs>
716 <param type="text" value="mm9" name="genome_name" label="Genome" help="(hg19, mm9, rn4, or other genomes supported by your NGS.plot installation)" >
717 </param>
718 <conditional name="genomic_region_source_type">
719 <param type="select" name="genomic_region" label="Genomic region" help="">
720 <option value="tss">TSS</option>
721 <option value="tes">TES</option>
722 <option value="genebody">Genebody</option>
723 <option value="exon">Exon</option>
724 <option value="cgi">CGI</option>
725 <option value="bed">Customized bed file</option>
726 </param>
727
728 <when value="tss">
729 <param type="select" name="further_information" label="Further information: Not required for TSS">
730 <option value="na">Not Required</option>
731 </param>
732 <param name="interval_size" type="select" label="Interval Region Size: Not required for TSS">
733 <option value="na">Not Required</option>
734 </param>
735 <conditional name="flanking_region_option_source_type">
736 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
737 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
738 <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option-->
739 </param>
740 <when value="flanking_region_size">
741 <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"/>
742 </when>
743 <!--when value="flanking_floating_size">
744 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
745 </when-->
746 </conditional>
747 </when>
748 <when value="tes">
749 <param type="select" name="further_information" label="Further information: Not required for TES">
750 <option value="na">Not Required</option>
751 </param>
752 <param name="interval_size" type="select" label="Interval Region Size: Not required for TES">
753 <option value="na">Not Required</option>
754 </param>
755 <conditional name="flanking_region_option_source_type">
756 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
757 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
758 <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option-->
759 </param>
760 <when value="flanking_region_size">
761 <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"/>
762 </when>
763 <!--when value="flanking_floating_size">
764 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
765 </when-->
766 </conditional>
767 </when>
768 <when value="genebody">
769 <param type="select" name="further_information" label="You selected Genebody, further information can be provided for specific regions to plot">
770 <option value="chipseq">ChIP-seq</option>
771 <option value="rnaseq">RNA-seq</option>
772 </param>
773 <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.">
774 <option value="automatic">Default</option>
775 <option value="0">Small</option>
776 <option value="1">Large</option>
777 </param>
778 <conditional name="flanking_region_option_source_type">
779 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
780 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
781 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
782 </param>
783 <when value="flanking_region_size">
784 <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"/>
785 </when>
786 <when value="flanking_floating_size">
787 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
788 </when>
789 </conditional>
790 </when>
791 <when value="exon">
792 <param type="select" name="further_information" label="You selected Exon, further information can be provided for specific regions to plot">
793 <option value="canonical">Canonical</option>
794 <option value="variant">Variant</option>
795 <option value="promoter">Promoter</option>
796 <option value="polyA">polyA</option>
797 <option value="altAcceptor">altAcceptor</option>
798 <option value="altDonor">altDonor</option>
799 <option value="altBoth">altBoth</option>
800 </param>
801 <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.">
802 <option value="automatic">Default</option>
803 <option value="0">Small</option>
804 <option value="1">Large</option>
805 </param>
806 <conditional name="flanking_region_option_source_type">
807 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
808 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
809 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
810 </param>
811 <when value="flanking_region_size">
812 <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"/>
813 </when>
814 <when value="flanking_floating_size">
815 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
816 </when>
817 </conditional>
818 </when>
819 <when value="cgi">
820 <param type="select" name="further_information" label="You select CGI, further information can be provided for specific regions to plot">
821 <option value="ProximalPromoter">ProximalPromoter</option>
822 <option value="Genebody">GeneBody</option>
823 <option value="Genedesert">GeneDesert</option>
824 <option value="OtherIntergenic">OtherIntergenic</option>
825 <option value="Pericentromere">Pericentromere</option>
826 <option value="Subtelomere">Subtelomere</option>
827 <option value="Promoter1k">Promoter1k</option>
828 <option value="Promoter3k">Promoter3k</option>
829 </param>
830 <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.">
831 <option value="automatic">Default</option>
832 <option value="0">Small</option>
833 <option value="1">Large</option>
834 </param>
835 <conditional name="flanking_region_option_source_type">
836 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
837 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
838 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
839 </param>
840 <when value="flanking_region_size">
841 <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"/>
842 </when>
843 <when value="flanking_floating_size">
844 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
845 </when>
846 </conditional>
847 </when>
848 <when value="bed">
849 <param type="select" name="further_information" label="Further information: Not required for bed input">
850 <option value="na">Not Required</option>
851 </param>
852 <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.">
853 <option value="automatic">Default</option>
854 <option value="0">Small</option>
855 <option value="1">Large</option>
856 </param>
857 <conditional name="flanking_region_option_source_type">
858 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
859 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
860 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
861 </param>
862 <when value="flanking_region_size">
863 <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"/>
864 </when>
865 <when value="flanking_floating_size">
866 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
867 </when>
868 </conditional>
869 </when>
870 </conditional>
871
872
873 <conditional name="numsamples">
874 <param type="select" name="numsamples2" label="Number of samples to plot">
875 <option value="1">1</option>
876 <option value="2">2</option>
877 <option value="3">3</option>
878 <option value="4">4</option>
879 <option value="5">5</option>
880 <option value="6">6</option>
881 <option value="7">7</option>
882 <option value="8">8</option>
883 <option value="9">9</option>
884 <option value="10">10</option>
885 </param>
886
887 <when value="1">
888 <conditional name="usepair">
889 <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.">
890 <option value="no">No</option>
891 <option value="yes">Yes</option>
892 </param>
893 <when value="no">
894 <!-- START: 1 sample, no refpairs, entry 1-->
895 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
896 <param type="hidden" name="reffile1" value="na"/>
897 <conditional name="genelist1">
898 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
899 <option value="no">Plot whole genome</option>
900 <option value="yes">Provide restricted gene list</option>
901 </param>
902 <when value="no">
903 <param type="hidden" name="genelist1" value="-1"/>
904 </when>
905 <when value="yes">
906 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
907 </when>
908 </conditional>
909 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
910 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
911 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
912 <!-- END: 1 sample, no refpairs, entry 1-->
913 </when>
914 <when value="yes">
915 <!-- START: 1 sample, yes refpairs, entry 1-->
916 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
917 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
918 <conditional name="genelist1">
919 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
920 <option value="no">Plot whole genome</option>
921 <option value="yes">Provide restricted gene list</option>
922 </param>
923 <when value="no">
924 <param type="hidden" name="genelist1" value="-1"/>
925 </when>
926 <when value="yes">
927 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
928 </when>
929 </conditional>
930 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
931 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
932 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
933 <!-- END: 1 sample, yes refpairs, entry 1-->
934 </when>
935 </conditional>
936 </when>
937 <when value="2">
938 <conditional name="usepair">
939 <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.">
940 <option value="no">No</option>
941 <option value="yes">Yes</option>
942 </param>
943 <when value="no">
944 <!-- START: 2 samples, no refpairs, entry 1-->
945 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
946 <param type="hidden" name="reffile1" value="na"/>
947 <conditional name="genelist1">
948 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
949 <option value="no">Plot whole genome</option>
950 <option value="yes">Provide restricted gene list</option>
951 </param>
952 <when value="no">
953 <param type="hidden" name="genelist1" value="-1"/>
954 </when>
955 <when value="yes">
956 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
957 </when>
958 </conditional>
959 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
960 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
961 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
962 <!-- END: 2 samples, no refpairs, entry 1-->
963 <!-- START: 2 samples, no refpairs, entry 2-->
964 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
965 <param type="hidden" name="reffile2" value="na"/>
966 <conditional name="genelist2">
967 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
968 <option value="no">Plot whole genome</option>
969 <option value="yes">Provide restricted gene list</option>
970 </param>
971 <when value="no">
972 <param type="hidden" name="genelist2" value="-1"/>
973 </when>
974 <when value="yes">
975 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
976 </when>
977 </conditional>
978 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
979 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
980 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
981 <!-- END: 2 samples, no refpairs, entry 2-->
982 </when>
983 <when value="yes">
984 <!-- START: 2 samples, yes refpairs, entry 1-->
985 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
986 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
987 <conditional name="genelist1">
988 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
989 <option value="no">Plot whole genome</option>
990 <option value="yes">Provide restricted gene list</option>
991 </param>
992 <when value="no">
993 <param type="hidden" name="genelist1" value="-1"/>
994 </when>
995 <when value="yes">
996 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
997 </when>
998 </conditional>
999 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1000 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1001 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1002 <!-- END: 2 samples, yes refpairs, entry 1-->
1003 <!-- START: 2 samples, yes refpairs, entry 2-->
1004 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1005 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1006 <conditional name="genelist2">
1007 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1008 <option value="no">Plot whole genome</option>
1009 <option value="yes">Provide restricted gene list</option>
1010 </param>
1011 <when value="no">
1012 <param type="hidden" name="genelist2" value="-1"/>
1013 </when>
1014 <when value="yes">
1015 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1016 </when>
1017 </conditional>
1018 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1019 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1020 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1021 <!-- END: 2 samples, yes refpairs, entry 2-->
1022 </when>
1023 </conditional>
1024 </when>
1025 <when value="3">
1026 <conditional name="usepair">
1027 <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.">
1028 <option value="no">No</option>
1029 <option value="yes">Yes</option>
1030 </param>
1031 <when value="no">
1032 <!-- START: 3 samples, no refpairs, entry 1-->
1033 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1034 <param type="hidden" name="reffile1" value="na"/>
1035 <conditional name="genelist1">
1036 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1037 <option value="no">Plot whole genome</option>
1038 <option value="yes">Provide restricted gene list</option>
1039 </param>
1040 <when value="no">
1041 <param type="hidden" name="genelist1" value="-1"/>
1042 </when>
1043 <when value="yes">
1044 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1045 </when>
1046 </conditional>
1047 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1048 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1049 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1050 <!-- END: 3 samples, no refpairs, entry 1-->
1051 <!-- START: 3 samples, no refpairs, entry 2-->
1052 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1053 <param type="hidden" name="reffile2" value="na"/>
1054 <conditional name="genelist2">
1055 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1056 <option value="no">Plot whole genome</option>
1057 <option value="yes">Provide restricted gene list</option>
1058 </param>
1059 <when value="no">
1060 <param type="hidden" name="genelist2" value="-1"/>
1061 </when>
1062 <when value="yes">
1063 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1064 </when>
1065 </conditional>
1066 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1067 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1068 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1069 <!-- END: 3 samples, no refpairs, entry 2-->
1070 <!-- START: 3 samples, no refpairs, entry 3-->
1071 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1072 <param type="hidden" name="reffile3" value="na"/>
1073 <conditional name="genelist3">
1074 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1075 <option value="no">Plot whole genome</option>
1076 <option value="yes">Provide restricted gene list</option>
1077 </param>
1078 <when value="no">
1079 <param type="hidden" name="genelist3" value="-1"/>
1080 </when>
1081 <when value="yes">
1082 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1083 </when>
1084 </conditional>
1085 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1086 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1087 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1088 <!-- END: 3 samples, no refpairs, entry 3-->
1089 </when>
1090 <when value="yes">
1091 <!-- START: 3 samples, yes refpairs, entry 1-->
1092 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1093 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1094 <conditional name="genelist1">
1095 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1096 <option value="no">Plot whole genome</option>
1097 <option value="yes">Provide restricted gene list</option>
1098 </param>
1099 <when value="no">
1100 <param type="hidden" name="genelist1" value="-1"/>
1101 </when>
1102 <when value="yes">
1103 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1104 </when>
1105 </conditional>
1106 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1107 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1108 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1109 <!-- END: 3 samples, yes refpairs, entry 1-->
1110 <!-- START: 3 samples, yes refpairs, entry 2-->
1111 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1112 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1113 <conditional name="genelist2">
1114 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1115 <option value="no">Plot whole genome</option>
1116 <option value="yes">Provide restricted gene list</option>
1117 </param>
1118 <when value="no">
1119 <param type="hidden" name="genelist2" value="-1"/>
1120 </when>
1121 <when value="yes">
1122 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1123 </when>
1124 </conditional>
1125 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1126 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1127 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1128 <!-- END: 3 samples, yes refpairs, entry 2-->
1129 <!-- START: 3 samples, yes refpairs, entry 3-->
1130 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1131 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1132 <conditional name="genelist3">
1133 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1134 <option value="no">Plot whole genome</option>
1135 <option value="yes">Provide restricted gene list</option>
1136 </param>
1137 <when value="no">
1138 <param type="hidden" name="genelist3" value="-1"/>
1139 </when>
1140 <when value="yes">
1141 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1142 </when>
1143 </conditional>
1144 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1145 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1146 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1147 <!-- END: 3 samples, yes refpairs, entry 2-->
1148 </when>
1149 </conditional>
1150 </when>
1151 <when value="4">
1152 <conditional name="usepair">
1153 <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.">
1154 <option value="no">No</option>
1155 <option value="yes">Yes</option>
1156 </param>
1157 <when value="no">
1158 <!-- START: 4 samples, no refpairs, entry 1-->
1159 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1160 <param type="hidden" name="reffile1" value="na"/>
1161 <conditional name="genelist1">
1162 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1163 <option value="no">Plot whole genome</option>
1164 <option value="yes">Provide restricted gene list</option>
1165 </param>
1166 <when value="no">
1167 <param type="hidden" name="genelist1" value="-1"/>
1168 </when>
1169 <when value="yes">
1170 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1171 </when>
1172 </conditional>
1173 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1174 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1175 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1176 <!-- END: 4 samples, no refpairs, entry 1-->
1177 <!-- START: 4 samples, no refpairs, entry 2-->
1178 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1179 <param type="hidden" name="reffile2" value="na"/>
1180 <conditional name="genelist2">
1181 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1182 <option value="no">Plot whole genome</option>
1183 <option value="yes">Provide restricted gene list</option>
1184 </param>
1185 <when value="no">
1186 <param type="hidden" name="genelist2" value="-1"/>
1187 </when>
1188 <when value="yes">
1189 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1190 </when>
1191 </conditional>
1192 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1193 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1194 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1195 <!-- END: 4 samples, no refpairs, entry 2-->
1196 <!-- START: 4 samples, no refpairs, entry 3-->
1197 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1198 <param type="hidden" name="reffile3" value="na"/>
1199 <conditional name="genelist3">
1200 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1201 <option value="no">Plot whole genome</option>
1202 <option value="yes">Provide restricted gene list</option>
1203 </param>
1204 <when value="no">
1205 <param type="hidden" name="genelist3" value="-1"/>
1206 </when>
1207 <when value="yes">
1208 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1209 </when>
1210 </conditional>
1211 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1212 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1213 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1214 <!-- END: 4 samples, no refpairs, entry 3-->
1215 <!-- START: 4 samples, no refpairs, entry 4-->
1216 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1217 <param type="hidden" name="reffile4" value="na"/>
1218 <conditional name="genelist4">
1219 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1220 <option value="no">Plot whole genome</option>
1221 <option value="yes">Provide restricted gene list</option>
1222 </param>
1223 <when value="no">
1224 <param type="hidden" name="genelist4" value="-1"/>
1225 </when>
1226 <when value="yes">
1227 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1228 </when>
1229 </conditional>
1230 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1231 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1232 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1233 <!-- END: 4 samples, no refpairs, entry 4-->
1234 </when>
1235 <when value="yes">
1236 <!-- START: 4 samples, yes refpairs, entry 1-->
1237 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1238 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1239 <conditional name="genelist1">
1240 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1241 <option value="no">Plot whole genome</option>
1242 <option value="yes">Provide restricted gene list</option>
1243 </param>
1244 <when value="no">
1245 <param type="hidden" name="genelist1" value="-1"/>
1246 </when>
1247 <when value="yes">
1248 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1249 </when>
1250 </conditional>
1251 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1252 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1253 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1254 <!-- END: 4 samples, yes refpairs, entry 1-->
1255 <!-- START: 4 samples, yes refpairs, entry 2-->
1256 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1257 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1258 <conditional name="genelist2">
1259 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1260 <option value="no">Plot whole genome</option>
1261 <option value="yes">Provide restricted gene list</option>
1262 </param>
1263 <when value="no">
1264 <param type="hidden" name="genelist2" value="-1"/>
1265 </when>
1266 <when value="yes">
1267 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1268 </when>
1269 </conditional>
1270 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1271 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1272 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1273 <!-- END: 4 samples, yes refpairs, entry 2-->
1274 <!-- START: 4 samples, yes refpairs, entry 3-->
1275 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1276 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1277 <conditional name="genelist3">
1278 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1279 <option value="no">Plot whole genome</option>
1280 <option value="yes">Provide restricted gene list</option>
1281 </param>
1282 <when value="no">
1283 <param type="hidden" name="genelist3" value="-1"/>
1284 </when>
1285 <when value="yes">
1286 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1287 </when>
1288 </conditional>
1289 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1290 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1291 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1292 <!-- END: 4 samples, yes refpairs, entry 3-->
1293 <!-- START: 4 samples, yes refpairs, entry 4-->
1294 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1295 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
1296 <conditional name="genelist4">
1297 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1298 <option value="no">Plot whole genome</option>
1299 <option value="yes">Provide restricted gene list</option>
1300 </param>
1301 <when value="no">
1302 <param type="hidden" name="genelist4" value="-1"/>
1303 </when>
1304 <when value="yes">
1305 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1306 </when>
1307 </conditional>
1308 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1309 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1310 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1311 <!-- END: 4 samples, yes refpairs, entry 4-->
1312 </when>
1313 </conditional>
1314 </when>
1315 <when value="5">
1316 <conditional name="usepair">
1317 <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.">
1318 <option value="no">No</option>
1319 <option value="yes">Yes</option>
1320 </param>
1321 <when value="no">
1322 <!-- START: 5 samples, no refpairs, entry 1-->
1323 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1324 <param type="hidden" name="reffile1" value="na"/>
1325 <conditional name="genelist1">
1326 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1327 <option value="no">Plot whole genome</option>
1328 <option value="yes">Provide restricted gene list</option>
1329 </param>
1330 <when value="no">
1331 <param type="hidden" name="genelist1" value="-1"/>
1332 </when>
1333 <when value="yes">
1334 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1335 </when>
1336 </conditional>
1337 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1338 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1339 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1340 <!-- END: 5 samples, no refpairs, entry 1-->
1341 <!-- START: 5 samples, no refpairs, entry 2-->
1342 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1343 <param type="hidden" name="reffile2" value="na"/>
1344 <conditional name="genelist2">
1345 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1346 <option value="no">Plot whole genome</option>
1347 <option value="yes">Provide restricted gene list</option>
1348 </param>
1349 <when value="no">
1350 <param type="hidden" name="genelist2" value="-1"/>
1351 </when>
1352 <when value="yes">
1353 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1354 </when>
1355 </conditional>
1356 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1357 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1358 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1359 <!-- END: 5 samples, no refpairs, entry 2-->
1360 <!-- START: 5 samples, no refpairs, entry 3-->
1361 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1362 <param type="hidden" name="reffile3" value="na"/>
1363 <conditional name="genelist3">
1364 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1365 <option value="no">Plot whole genome</option>
1366 <option value="yes">Provide restricted gene list</option>
1367 </param>
1368 <when value="no">
1369 <param type="hidden" name="genelist3" value="-1"/>
1370 </when>
1371 <when value="yes">
1372 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1373 </when>
1374 </conditional>
1375 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1376 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1377 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1378 <!-- END: 5 samples, no refpairs, entry 3-->
1379 <!-- START: 5 samples, no refpairs, entry 4-->
1380 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1381 <param type="hidden" name="reffile4" value="na"/>
1382 <conditional name="genelist4">
1383 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1384 <option value="no">Plot whole genome</option>
1385 <option value="yes">Provide restricted gene list</option>
1386 </param>
1387 <when value="no">
1388 <param type="hidden" name="genelist4" value="-1"/>
1389 </when>
1390 <when value="yes">
1391 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1392 </when>
1393 </conditional>
1394 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1395 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1396 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1397 <!-- END: 5 samples, no refpairs, entry 4-->
1398 <!-- START: 5 samples, no refpairs, entry 5-->
1399 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1400 <param type="hidden" name="reffile5" value="na"/>
1401 <conditional name="genelist5">
1402 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1403 <option value="no">Plot whole genome</option>
1404 <option value="yes">Provide restricted gene list</option>
1405 </param>
1406 <when value="no">
1407 <param type="hidden" name="genelist5" value="-1"/>
1408 </when>
1409 <when value="yes">
1410 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1411 </when>
1412 </conditional>
1413 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1414 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1415 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1416 <!-- END: 5 samples, no refpairs, entry 5-->
1417 </when>
1418 <when value="yes">
1419 <!-- START: 5 samples, yes refpairs, entry 1-->
1420 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1421 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1422 <conditional name="genelist1">
1423 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1424 <option value="no">Plot whole genome</option>
1425 <option value="yes">Provide restricted gene list</option>
1426 </param>
1427 <when value="no">
1428 <param type="hidden" name="genelist1" value="-1"/>
1429 </when>
1430 <when value="yes">
1431 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1432 </when>
1433 </conditional>
1434 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1435 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1436 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1437 <!-- END: 5 samples, yes refpairs, entry 1-->
1438 <!-- START: 5 samples, yes refpairs, entry 2-->
1439 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1440 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1441 <conditional name="genelist2">
1442 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1443 <option value="no">Plot whole genome</option>
1444 <option value="yes">Provide restricted gene list</option>
1445 </param>
1446 <when value="no">
1447 <param type="hidden" name="genelist2" value="-1"/>
1448 </when>
1449 <when value="yes">
1450 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1451 </when>
1452 </conditional>
1453 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1454 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1455 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1456 <!-- END: 5 samples, yes refpairs, entry 2-->
1457 <!-- START: 5 samples, yes refpairs, entry 3-->
1458 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1459 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1460 <conditional name="genelist3">
1461 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1462 <option value="no">Plot whole genome</option>
1463 <option value="yes">Provide restricted gene list</option>
1464 </param>
1465 <when value="no">
1466 <param type="hidden" name="genelist3" value="-1"/>
1467 </when>
1468 <when value="yes">
1469 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1470 </when>
1471 </conditional>
1472 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1473 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1474 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1475 <!-- END: 5 samples, yes refpairs, entry 3-->
1476 <!-- START: 5 samples, yes refpairs, entry 4-->
1477 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1478 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
1479 <conditional name="genelist4">
1480 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1481 <option value="no">Plot whole genome</option>
1482 <option value="yes">Provide restricted gene list</option>
1483 </param>
1484 <when value="no">
1485 <param type="hidden" name="genelist4" value="-1"/>
1486 </when>
1487 <when value="yes">
1488 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1489 </when>
1490 </conditional>
1491 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1492 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1493 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1494 <!-- END: 5 samples, yes refpairs, entry 4-->
1495 <!-- START: 5 samples, yes refpairs, entry 5-->
1496 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1497 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
1498 <conditional name="genelist5">
1499 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1500 <option value="no">Plot whole genome</option>
1501 <option value="yes">Provide restricted gene list</option>
1502 </param>
1503 <when value="no">
1504 <param type="hidden" name="genelist5" value="-1"/>
1505 </when>
1506 <when value="yes">
1507 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1508 </when>
1509 </conditional>
1510 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1511 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1512 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1513 <!-- END: 5 samples, yes refpairs, entry 5-->
1514 </when>
1515 </conditional>
1516 </when>
1517 <when value="6">
1518 <conditional name="usepair">
1519 <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.">
1520 <option value="no">No</option>
1521 <option value="yes">Yes</option>
1522 </param>
1523 <when value="no">
1524 <!-- START: 6 samples, no refpairs, entry 1-->
1525 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1526 <param type="hidden" name="reffile1" value="na"/>
1527 <conditional name="genelist1">
1528 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1529 <option value="no">Plot whole genome</option>
1530 <option value="yes">Provide restricted gene list</option>
1531 </param>
1532 <when value="no">
1533 <param type="hidden" name="genelist1" value="-1"/>
1534 </when>
1535 <when value="yes">
1536 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1537 </when>
1538 </conditional>
1539 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1540 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1541 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1542 <!-- END: 6 samples, no refpairs, entry 1-->
1543 <!-- START: 6 samples, no refpairs, entry 2-->
1544 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1545 <param type="hidden" name="reffile2" value="na"/>
1546 <conditional name="genelist2">
1547 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1548 <option value="no">Plot whole genome</option>
1549 <option value="yes">Provide restricted gene list</option>
1550 </param>
1551 <when value="no">
1552 <param type="hidden" name="genelist2" value="-1"/>
1553 </when>
1554 <when value="yes">
1555 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1556 </when>
1557 </conditional>
1558 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1559 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1560 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1561 <!-- END: 6 samples, no refpairs, entry 2-->
1562 <!-- START: 6 samples, no refpairs, entry 3-->
1563 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1564 <param type="hidden" name="reffile3" value="na"/>
1565 <conditional name="genelist3">
1566 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1567 <option value="no">Plot whole genome</option>
1568 <option value="yes">Provide restricted gene list</option>
1569 </param>
1570 <when value="no">
1571 <param type="hidden" name="genelist3" value="-1"/>
1572 </when>
1573 <when value="yes">
1574 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1575 </when>
1576 </conditional>
1577 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1578 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1579 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1580 <!-- END: 6 samples, no refpairs, entry 3-->
1581 <!-- START: 6 samples, no refpairs, entry 4-->
1582 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1583 <param type="hidden" name="reffile4" value="na"/>
1584 <conditional name="genelist4">
1585 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1586 <option value="no">Plot whole genome</option>
1587 <option value="yes">Provide restricted gene list</option>
1588 </param>
1589 <when value="no">
1590 <param type="hidden" name="genelist4" value="-1"/>
1591 </when>
1592 <when value="yes">
1593 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1594 </when>
1595 </conditional>
1596 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1597 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1598 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1599 <!-- END: 6 samples, no refpairs, entry 4-->
1600 <!-- START: 6 samples, no refpairs, entry 5-->
1601 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1602 <param type="hidden" name="reffile5" value="na"/>
1603 <conditional name="genelist5">
1604 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1605 <option value="no">Plot whole genome</option>
1606 <option value="yes">Provide restricted gene list</option>
1607 </param>
1608 <when value="no">
1609 <param type="hidden" name="genelist5" value="-1"/>
1610 </when>
1611 <when value="yes">
1612 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1613 </when>
1614 </conditional>
1615 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1616 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1617 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1618 <!-- END: 6 samples, no refpairs, entry 5-->
1619 <!-- START: 6 samples, no refpairs, entry 6-->
1620 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
1621 <param type="hidden" name="reffile6" value="na"/>
1622 <conditional name="genelist6">
1623 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
1624 <option value="no">Plot whole genome</option>
1625 <option value="yes">Provide restricted gene list</option>
1626 </param>
1627 <when value="no">
1628 <param type="hidden" name="genelist6" value="-1"/>
1629 </when>
1630 <when value="yes">
1631 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
1632 </when>
1633 </conditional>
1634 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
1635 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
1636 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
1637 <!-- END: 6 samples, no refpairs, entry 6-->
1638 </when>
1639 <when value="yes">
1640 <!-- START: 6 samples, yes refpairs, entry 1-->
1641 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1642 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1643 <conditional name="genelist1">
1644 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1645 <option value="no">Plot whole genome</option>
1646 <option value="yes">Provide restricted gene list</option>
1647 </param>
1648 <when value="no">
1649 <param type="hidden" name="genelist1" value="-1"/>
1650 </when>
1651 <when value="yes">
1652 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1653 </when>
1654 </conditional>
1655 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1656 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1657 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1658 <!-- END: 6 samples, yes refpairs, entry 1-->
1659 <!-- START: 6 samples, yes refpairs, entry 2-->
1660 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1661 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1662 <conditional name="genelist2">
1663 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1664 <option value="no">Plot whole genome</option>
1665 <option value="yes">Provide restricted gene list</option>
1666 </param>
1667 <when value="no">
1668 <param type="hidden" name="genelist2" value="-1"/>
1669 </when>
1670 <when value="yes">
1671 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1672 </when>
1673 </conditional>
1674 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1675 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1676 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1677 <!-- END: 6 samples, yes refpairs, entry 2-->
1678 <!-- START: 6 samples, yes refpairs, entry 3-->
1679 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1680 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1681 <conditional name="genelist3">
1682 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1683 <option value="no">Plot whole genome</option>
1684 <option value="yes">Provide restricted gene list</option>
1685 </param>
1686 <when value="no">
1687 <param type="hidden" name="genelist3" value="-1"/>
1688 </when>
1689 <when value="yes">
1690 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1691 </when>
1692 </conditional>
1693 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1694 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1695 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1696 <!-- END: 6 samples, yes refpairs, entry 3-->
1697 <!-- START: 6 samples, yes refpairs, entry 4-->
1698 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1699 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
1700 <conditional name="genelist4">
1701 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1702 <option value="no">Plot whole genome</option>
1703 <option value="yes">Provide restricted gene list</option>
1704 </param>
1705 <when value="no">
1706 <param type="hidden" name="genelist4" value="-1"/>
1707 </when>
1708 <when value="yes">
1709 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1710 </when>
1711 </conditional>
1712 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1713 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1714 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1715 <!-- END: 6 samples, yes refpairs, entry 4-->
1716 <!-- START: 6 samples, yes refpairs, entry 5-->
1717 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1718 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
1719 <conditional name="genelist5">
1720 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1721 <option value="no">Plot whole genome</option>
1722 <option value="yes">Provide restricted gene list</option>
1723 </param>
1724 <when value="no">
1725 <param type="hidden" name="genelist5" value="-1"/>
1726 </when>
1727 <when value="yes">
1728 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1729 </when>
1730 </conditional>
1731 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1732 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1733 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1734 <!-- END: 6 samples, yes refpairs, entry 5-->
1735 <!-- START: 6 samples, yes refpairs, entry 6-->
1736 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
1737 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
1738 <conditional name="genelist6">
1739 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
1740 <option value="no">Plot whole genome</option>
1741 <option value="yes">Provide restricted gene list</option>
1742 </param>
1743 <when value="no">
1744 <param type="hidden" name="genelist6" value="-1"/>
1745 </when>
1746 <when value="yes">
1747 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
1748 </when>
1749 </conditional>
1750 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
1751 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
1752 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
1753 <!-- END: 6 samples, yes refpairs, entry 6-->
1754 </when>
1755 </conditional>
1756 </when>
1757 <when value="7">
1758 <conditional name="usepair">
1759 <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.">
1760 <option value="no">No</option>
1761 <option value="yes">Yes</option>
1762 </param>
1763 <when value="no">
1764 <!-- START: 7 samples, no refpairs, entry 1-->
1765 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1766 <param type="hidden" name="reffile1" value="na"/>
1767 <conditional name="genelist1">
1768 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1769 <option value="no">Plot whole genome</option>
1770 <option value="yes">Provide restricted gene list</option>
1771 </param>
1772 <when value="no">
1773 <param type="hidden" name="genelist1" value="-1"/>
1774 </when>
1775 <when value="yes">
1776 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1777 </when>
1778 </conditional>
1779 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1780 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1781 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1782 <!-- END: 7 samples, no refpairs, entry 1-->
1783 <!-- START: 7 samples, no refpairs, entry 2-->
1784 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1785 <param type="hidden" name="reffile2" value="na"/>
1786 <conditional name="genelist2">
1787 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1788 <option value="no">Plot whole genome</option>
1789 <option value="yes">Provide restricted gene list</option>
1790 </param>
1791 <when value="no">
1792 <param type="hidden" name="genelist2" value="-1"/>
1793 </when>
1794 <when value="yes">
1795 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1796 </when>
1797 </conditional>
1798 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1799 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1800 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1801 <!-- END: 7 samples, no refpairs, entry 2-->
1802 <!-- START: 7 samples, no refpairs, entry 3-->
1803 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1804 <param type="hidden" name="reffile3" value="na"/>
1805 <conditional name="genelist3">
1806 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1807 <option value="no">Plot whole genome</option>
1808 <option value="yes">Provide restricted gene list</option>
1809 </param>
1810 <when value="no">
1811 <param type="hidden" name="genelist3" value="-1"/>
1812 </when>
1813 <when value="yes">
1814 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1815 </when>
1816 </conditional>
1817 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1818 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1819 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1820 <!-- END: 7 samples, no refpairs, entry 3-->
1821 <!-- START: 7 samples, no refpairs, entry 4-->
1822 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1823 <param type="hidden" name="reffile4" value="na"/>
1824 <conditional name="genelist4">
1825 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1826 <option value="no">Plot whole genome</option>
1827 <option value="yes">Provide restricted gene list</option>
1828 </param>
1829 <when value="no">
1830 <param type="hidden" name="genelist4" value="-1"/>
1831 </when>
1832 <when value="yes">
1833 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1834 </when>
1835 </conditional>
1836 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1837 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1838 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1839 <!-- END: 7 samples, no refpairs, entry 4-->
1840 <!-- START: 7 samples, no refpairs, entry 5-->
1841 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1842 <param type="hidden" name="reffile5" value="na"/>
1843 <conditional name="genelist5">
1844 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1845 <option value="no">Plot whole genome</option>
1846 <option value="yes">Provide restricted gene list</option>
1847 </param>
1848 <when value="no">
1849 <param type="hidden" name="genelist5" value="-1"/>
1850 </when>
1851 <when value="yes">
1852 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1853 </when>
1854 </conditional>
1855 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1856 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1857 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1858 <!-- END: 7 samples, no refpairs, entry 5-->
1859 <!-- START: 7 samples, no refpairs, entry 6-->
1860 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
1861 <param type="hidden" name="reffile6" value="na"/>
1862 <conditional name="genelist6">
1863 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
1864 <option value="no">Plot whole genome</option>
1865 <option value="yes">Provide restricted gene list</option>
1866 </param>
1867 <when value="no">
1868 <param type="hidden" name="genelist6" value="-1"/>
1869 </when>
1870 <when value="yes">
1871 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
1872 </when>
1873 </conditional>
1874 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
1875 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
1876 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
1877 <!-- END: 7 samples, no refpairs, entry 6-->
1878 <!-- START: 7 samples, no refpairs, entry 7-->
1879 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
1880 <param type="hidden" name="reffile7" value="na"/>
1881 <conditional name="genelist7">
1882 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
1883 <option value="no">Plot whole genome</option>
1884 <option value="yes">Provide restricted gene list</option>
1885 </param>
1886 <when value="no">
1887 <param type="hidden" name="genelist7" value="-1"/>
1888 </when>
1889 <when value="yes">
1890 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
1891 </when>
1892 </conditional>
1893 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
1894 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
1895 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
1896 <!-- END: 7 samples, no refpairs, entry 7-->
1897 </when>
1898 <when value="yes">
1899 <!-- START: 7 samples, yes refpairs, entry 1-->
1900 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1901 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1902 <conditional name="genelist1">
1903 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1904 <option value="no">Plot whole genome</option>
1905 <option value="yes">Provide restricted gene list</option>
1906 </param>
1907 <when value="no">
1908 <param type="hidden" name="genelist1" value="-1"/>
1909 </when>
1910 <when value="yes">
1911 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1912 </when>
1913 </conditional>
1914 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1915 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1916 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1917 <!-- END: 7 samples, yes refpairs, entry 1-->
1918 <!-- START: 7 samples, yes refpairs, entry 2-->
1919 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1920 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1921 <conditional name="genelist2">
1922 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1923 <option value="no">Plot whole genome</option>
1924 <option value="yes">Provide restricted gene list</option>
1925 </param>
1926 <when value="no">
1927 <param type="hidden" name="genelist2" value="-1"/>
1928 </when>
1929 <when value="yes">
1930 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1931 </when>
1932 </conditional>
1933 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1934 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1935 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1936 <!-- END: 7 samples, yes refpairs, entry 2-->
1937 <!-- START: 7 samples, yes refpairs, entry 3-->
1938 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1939 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1940 <conditional name="genelist3">
1941 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1942 <option value="no">Plot whole genome</option>
1943 <option value="yes">Provide restricted gene list</option>
1944 </param>
1945 <when value="no">
1946 <param type="hidden" name="genelist3" value="-1"/>
1947 </when>
1948 <when value="yes">
1949 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1950 </when>
1951 </conditional>
1952 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1953 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1954 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1955 <!-- END: 7 samples, yes refpairs, entry 3-->
1956 <!-- START: 7 samples, yes refpairs, entry 4-->
1957 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1958 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
1959 <conditional name="genelist4">
1960 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1961 <option value="no">Plot whole genome</option>
1962 <option value="yes">Provide restricted gene list</option>
1963 </param>
1964 <when value="no">
1965 <param type="hidden" name="genelist4" value="-1"/>
1966 </when>
1967 <when value="yes">
1968 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1969 </when>
1970 </conditional>
1971 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1972 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1973 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1974 <!-- END: 7 samples, yes refpairs, entry 4-->
1975 <!-- START: 7 samples, yes refpairs, entry 5-->
1976 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1977 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
1978 <conditional name="genelist5">
1979 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1980 <option value="no">Plot whole genome</option>
1981 <option value="yes">Provide restricted gene list</option>
1982 </param>
1983 <when value="no">
1984 <param type="hidden" name="genelist5" value="-1"/>
1985 </when>
1986 <when value="yes">
1987 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1988 </when>
1989 </conditional>
1990 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1991 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1992 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1993 <!-- END: 7 samples, yes refpairs, entry 5-->
1994 <!-- START: 7 samples, yes refpairs, entry 6-->
1995 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
1996 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
1997 <conditional name="genelist6">
1998 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
1999 <option value="no">Plot whole genome</option>
2000 <option value="yes">Provide restricted gene list</option>
2001 </param>
2002 <when value="no">
2003 <param type="hidden" name="genelist6" value="-1"/>
2004 </when>
2005 <when value="yes">
2006 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2007 </when>
2008 </conditional>
2009 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2010 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2011 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2012 <!-- END: 7 samples, yes refpairs, entry 6-->
2013 <!-- START: 7 samples, yes refpairs, entry 7-->
2014 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2015 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
2016 <conditional name="genelist7">
2017 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2018 <option value="no">Plot whole genome</option>
2019 <option value="yes">Provide restricted gene list</option>
2020 </param>
2021 <when value="no">
2022 <param type="hidden" name="genelist7" value="-1"/>
2023 </when>
2024 <when value="yes">
2025 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2026 </when>
2027 </conditional>
2028 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2029 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2030 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2031 <!-- END: 7 samples, yes refpairs, entry 7-->
2032 </when>
2033 </conditional>
2034 </when>
2035 <when value="8">
2036 <conditional name="usepair">
2037 <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.">
2038 <option value="no">No</option>
2039 <option value="yes">Yes</option>
2040 </param>
2041 <when value="no">
2042 <!-- START: 8 samples, no refpairs, entry 1-->
2043 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2044 <param type="hidden" name="reffile1" value="na"/>
2045 <conditional name="genelist1">
2046 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2047 <option value="no">Plot whole genome</option>
2048 <option value="yes">Provide restricted gene list</option>
2049 </param>
2050 <when value="no">
2051 <param type="hidden" name="genelist1" value="-1"/>
2052 </when>
2053 <when value="yes">
2054 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2055 </when>
2056 </conditional>
2057 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2058 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2059 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2060 <!-- END: 8 samples, no refpairs, entry 1-->
2061 <!-- START: 8 samples, no refpairs, entry 2-->
2062 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2063 <param type="hidden" name="reffile2" value="na"/>
2064 <conditional name="genelist2">
2065 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2066 <option value="no">Plot whole genome</option>
2067 <option value="yes">Provide restricted gene list</option>
2068 </param>
2069 <when value="no">
2070 <param type="hidden" name="genelist2" value="-1"/>
2071 </when>
2072 <when value="yes">
2073 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2074 </when>
2075 </conditional>
2076 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2077 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2078 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2079 <!-- END: 8 samples, no refpairs, entry 2-->
2080 <!-- START: 8 samples, no refpairs, entry 3-->
2081 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2082 <param type="hidden" name="reffile3" value="na"/>
2083 <conditional name="genelist3">
2084 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2085 <option value="no">Plot whole genome</option>
2086 <option value="yes">Provide restricted gene list</option>
2087 </param>
2088 <when value="no">
2089 <param type="hidden" name="genelist3" value="-1"/>
2090 </when>
2091 <when value="yes">
2092 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2093 </when>
2094 </conditional>
2095 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2096 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2097 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2098 <!-- END: 8 samples, no refpairs, entry 3-->
2099 <!-- START: 8 samples, no refpairs, entry 4-->
2100 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2101 <param type="hidden" name="reffile4" value="na"/>
2102 <conditional name="genelist4">
2103 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2104 <option value="no">Plot whole genome</option>
2105 <option value="yes">Provide restricted gene list</option>
2106 </param>
2107 <when value="no">
2108 <param type="hidden" name="genelist4" value="-1"/>
2109 </when>
2110 <when value="yes">
2111 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2112 </when>
2113 </conditional>
2114 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2115 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2116 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2117 <!-- END: 8 samples, no refpairs, entry 4-->
2118 <!-- START: 8 samples, no refpairs, entry 5-->
2119 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2120 <param type="hidden" name="reffile5" value="na"/>
2121 <conditional name="genelist5">
2122 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2123 <option value="no">Plot whole genome</option>
2124 <option value="yes">Provide restricted gene list</option>
2125 </param>
2126 <when value="no">
2127 <param type="hidden" name="genelist5" value="-1"/>
2128 </when>
2129 <when value="yes">
2130 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2131 </when>
2132 </conditional>
2133 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2134 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2135 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2136 <!-- END: 8 samples, no refpairs, entry 5-->
2137 <!-- START: 8 samples, no refpairs, entry 6-->
2138 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2139 <param type="hidden" name="reffile6" value="na"/>
2140 <conditional name="genelist6">
2141 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2142 <option value="no">Plot whole genome</option>
2143 <option value="yes">Provide restricted gene list</option>
2144 </param>
2145 <when value="no">
2146 <param type="hidden" name="genelist6" value="-1"/>
2147 </when>
2148 <when value="yes">
2149 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2150 </when>
2151 </conditional>
2152 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2153 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2154 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2155 <!-- END: 8 samples, no refpairs, entry 6-->
2156 <!-- START: 8 samples, no refpairs, entry 7-->
2157 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2158 <param type="hidden" name="reffile7" value="na"/>
2159 <conditional name="genelist7">
2160 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2161 <option value="no">Plot whole genome</option>
2162 <option value="yes">Provide restricted gene list</option>
2163 </param>
2164 <when value="no">
2165 <param type="hidden" name="genelist7" value="-1"/>
2166 </when>
2167 <when value="yes">
2168 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2169 </when>
2170 </conditional>
2171 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2172 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2173 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2174 <!-- END: 8 samples, no refpairs, entry 7-->
2175 <!-- START: 8 samples, no refpairs, entry 8-->
2176 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2177 <param type="hidden" name="reffile8" value="na"/>
2178 <conditional name="genelist7">
2179 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2180 <option value="no">Plot whole genome</option>
2181 <option value="yes">Provide restricted gene list</option>
2182 </param>
2183 <when value="no">
2184 <param type="hidden" name="genelist8" value="-1"/>
2185 </when>
2186 <when value="yes">
2187 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2188 </when>
2189 </conditional>
2190 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2191 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2192 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2193 <!-- END: 8 samples, no refpairs, entry 8-->
2194 </when>
2195 <when value="yes">
2196 <!-- START: 8 samples, yes refpairs, entry 1-->
2197 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2198 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
2199 <conditional name="genelist1">
2200 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2201 <option value="no">Plot whole genome</option>
2202 <option value="yes">Provide restricted gene list</option>
2203 </param>
2204 <when value="no">
2205 <param type="hidden" name="genelist1" value="-1"/>
2206 </when>
2207 <when value="yes">
2208 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2209 </when>
2210 </conditional>
2211 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2212 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2213 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2214 <!-- END: 8 samples, yes refpairs, entry 1-->
2215 <!-- START: 8 samples, yes refpairs, entry 2-->
2216 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2217 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
2218 <conditional name="genelist2">
2219 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2220 <option value="no">Plot whole genome</option>
2221 <option value="yes">Provide restricted gene list</option>
2222 </param>
2223 <when value="no">
2224 <param type="hidden" name="genelist2" value="-1"/>
2225 </when>
2226 <when value="yes">
2227 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2228 </when>
2229 </conditional>
2230 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2231 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2232 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2233 <!-- END: 8 samples, yes refpairs, entry 2-->
2234 <!-- START: 8 samples, yes refpairs, entry 3-->
2235 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2236 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
2237 <conditional name="genelist3">
2238 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2239 <option value="no">Plot whole genome</option>
2240 <option value="yes">Provide restricted gene list</option>
2241 </param>
2242 <when value="no">
2243 <param type="hidden" name="genelist3" value="-1"/>
2244 </when>
2245 <when value="yes">
2246 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2247 </when>
2248 </conditional>
2249 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2250 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2251 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2252 <!-- END: 8 samples, yes refpairs, entry 3-->
2253 <!-- START: 8 samples, yes refpairs, entry 4-->
2254 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2255 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
2256 <conditional name="genelist4">
2257 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2258 <option value="no">Plot whole genome</option>
2259 <option value="yes">Provide restricted gene list</option>
2260 </param>
2261 <when value="no">
2262 <param type="hidden" name="genelist4" value="-1"/>
2263 </when>
2264 <when value="yes">
2265 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2266 </when>
2267 </conditional>
2268 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2269 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2270 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2271 <!-- END: 8 samples, yes refpairs, entry 4-->
2272 <!-- START: 8 samples, yes refpairs, entry 5-->
2273 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2274 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
2275 <conditional name="genelist5">
2276 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2277 <option value="no">Plot whole genome</option>
2278 <option value="yes">Provide restricted gene list</option>
2279 </param>
2280 <when value="no">
2281 <param type="hidden" name="genelist5" value="-1"/>
2282 </when>
2283 <when value="yes">
2284 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2285 </when>
2286 </conditional>
2287 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2288 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2289 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2290 <!-- END: 8 samples, yes refpairs, entry 5-->
2291 <!-- START: 8 samples, yes refpairs, entry 6-->
2292 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2293 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
2294 <conditional name="genelist6">
2295 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2296 <option value="no">Plot whole genome</option>
2297 <option value="yes">Provide restricted gene list</option>
2298 </param>
2299 <when value="no">
2300 <param type="hidden" name="genelist6" value="-1"/>
2301 </when>
2302 <when value="yes">
2303 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2304 </when>
2305 </conditional>
2306 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2307 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2308 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2309 <!-- END: 8 samples, yes refpairs, entry 6-->
2310 <!-- START: 8 samples, yes refpairs, entry 7-->
2311 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2312 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
2313 <conditional name="genelist7">
2314 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2315 <option value="no">Plot whole genome</option>
2316 <option value="yes">Provide restricted gene list</option>
2317 </param>
2318 <when value="no">
2319 <param type="hidden" name="genelist7" value="-1"/>
2320 </when>
2321 <when value="yes">
2322 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2323 </when>
2324 </conditional>
2325 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2326 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2327 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2328 <!-- END: 8 samples, yes refpairs, entry 7-->
2329 <!-- START: 8 samples, yes refpairs, entry 8-->
2330 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2331 <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/>
2332 <conditional name="genelist8">
2333 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2334 <option value="no">Plot whole genome</option>
2335 <option value="yes">Provide restricted gene list</option>
2336 </param>
2337 <when value="no">
2338 <param type="hidden" name="genelist8" value="-1"/>
2339 </when>
2340 <when value="yes">
2341 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2342 </when>
2343 </conditional>
2344 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2345 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2346 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2347 <!-- END: 8 samples, yes refpairs, entry 8-->
2348 </when>
2349 </conditional>
2350 </when>
2351 <when value="9">
2352 <conditional name="usepair">
2353 <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.">
2354 <option value="no">No</option>
2355 <option value="yes">Yes</option>
2356 </param>
2357 <when value="no">
2358 <!-- START: 9 samples, no refpairs, entry 1-->
2359 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2360 <param type="hidden" name="reffile1" value="na"/>
2361 <conditional name="genelist1">
2362 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2363 <option value="no">Plot whole genome</option>
2364 <option value="yes">Provide restricted gene list</option>
2365 </param>
2366 <when value="no">
2367 <param type="hidden" name="genelist1" value="-1"/>
2368 </when>
2369 <when value="yes">
2370 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2371 </when>
2372 </conditional>
2373 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2374 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2375 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2376 <!-- END: 9 samples, no refpairs, entry 1-->
2377 <!-- START: 9 samples, no refpairs, entry 2-->
2378 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2379 <param type="hidden" name="reffile2" value="na"/>
2380 <conditional name="genelist2">
2381 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2382 <option value="no">Plot whole genome</option>
2383 <option value="yes">Provide restricted gene list</option>
2384 </param>
2385 <when value="no">
2386 <param type="hidden" name="genelist2" value="-1"/>
2387 </when>
2388 <when value="yes">
2389 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2390 </when>
2391 </conditional>
2392 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2393 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2394 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2395 <!-- END: 9 samples, no refpairs, entry 2-->
2396 <!-- START: 9 samples, no refpairs, entry 3-->
2397 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2398 <param type="hidden" name="reffile3" value="na"/>
2399 <conditional name="genelist3">
2400 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2401 <option value="no">Plot whole genome</option>
2402 <option value="yes">Provide restricted gene list</option>
2403 </param>
2404 <when value="no">
2405 <param type="hidden" name="genelist3" value="-1"/>
2406 </when>
2407 <when value="yes">
2408 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2409 </when>
2410 </conditional>
2411 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2412 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2413 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2414 <!-- END: 9 samples, no refpairs, entry 3-->
2415 <!-- START: 9 samples, no refpairs, entry 4-->
2416 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2417 <param type="hidden" name="reffile4" value="na"/>
2418 <conditional name="genelist4">
2419 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2420 <option value="no">Plot whole genome</option>
2421 <option value="yes">Provide restricted gene list</option>
2422 </param>
2423 <when value="no">
2424 <param type="hidden" name="genelist4" value="-1"/>
2425 </when>
2426 <when value="yes">
2427 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2428 </when>
2429 </conditional>
2430 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2431 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2432 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2433 <!-- END: 9 samples, no refpairs, entry 4-->
2434 <!-- START: 9 samples, no refpairs, entry 5-->
2435 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2436 <param type="hidden" name="reffile5" value="na"/>
2437 <conditional name="genelist5">
2438 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2439 <option value="no">Plot whole genome</option>
2440 <option value="yes">Provide restricted gene list</option>
2441 </param>
2442 <when value="no">
2443 <param type="hidden" name="genelist5" value="-1"/>
2444 </when>
2445 <when value="yes">
2446 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2447 </when>
2448 </conditional>
2449 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2450 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2451 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2452 <!-- END: 9 samples, no refpairs, entry 5-->
2453 <!-- START: 9 samples, no refpairs, entry 6-->
2454 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2455 <param type="hidden" name="reffile6" value="na"/>
2456 <conditional name="genelist6">
2457 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2458 <option value="no">Plot whole genome</option>
2459 <option value="yes">Provide restricted gene list</option>
2460 </param>
2461 <when value="no">
2462 <param type="hidden" name="genelist6" value="-1"/>
2463 </when>
2464 <when value="yes">
2465 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2466 </when>
2467 </conditional>
2468 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2469 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2470 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2471 <!-- END: 9 samples, no refpairs, entry 6-->
2472 <!-- START: 9 samples, no refpairs, entry 7-->
2473 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2474 <param type="hidden" name="reffile7" value="na"/>
2475 <conditional name="genelist7">
2476 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2477 <option value="no">Plot whole genome</option>
2478 <option value="yes">Provide restricted gene list</option>
2479 </param>
2480 <when value="no">
2481 <param type="hidden" name="genelist7" value="-1"/>
2482 </when>
2483 <when value="yes">
2484 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2485 </when>
2486 </conditional>
2487 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2488 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2489 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2490 <!-- END: 9 samples, no refpairs, entry 7-->
2491 <!-- START: 9 samples, no refpairs, entry 8-->
2492 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2493 <param type="hidden" name="reffile8" value="na"/>
2494 <conditional name="genelist8">
2495 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2496 <option value="no">Plot whole genome</option>
2497 <option value="yes">Provide restricted gene list</option>
2498 </param>
2499 <when value="no">
2500 <param type="hidden" name="genelist8" value="-1"/>
2501 </when>
2502 <when value="yes">
2503 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2504 </when>
2505 </conditional>
2506 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2507 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2508 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2509 <!-- END: 9 samples, no refpairs, entry 8-->
2510 <!-- START: 9 samples, no refpairs, entry 9-->
2511 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
2512 <param type="hidden" name="reffile9" value="na"/>
2513 <conditional name="genelist9">
2514 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
2515 <option value="no">Plot whole genome</option>
2516 <option value="yes">Provide restricted gene list</option>
2517 </param>
2518 <when value="no">
2519 <param type="hidden" name="genelist9" value="-1"/>
2520 </when>
2521 <when value="yes">
2522 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
2523 </when>
2524 </conditional>
2525 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
2526 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
2527 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
2528 <!-- END: 9 samples, no refpairs, entry 9-->
2529 </when>
2530 <when value="yes">
2531 <!-- START: 9 samples, yes refpairs, entry 1-->
2532 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2533 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
2534 <conditional name="genelist1">
2535 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2536 <option value="no">Plot whole genome</option>
2537 <option value="yes">Provide restricted gene list</option>
2538 </param>
2539 <when value="no">
2540 <param type="hidden" name="genelist1" value="-1"/>
2541 </when>
2542 <when value="yes">
2543 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2544 </when>
2545 </conditional>
2546 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2547 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2548 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2549 <!-- END: 9 samples, yes refpairs, entry 1-->
2550 <!-- START: 9 samples, yes refpairs, entry 2-->
2551 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2552 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
2553 <conditional name="genelist2">
2554 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2555 <option value="no">Plot whole genome</option>
2556 <option value="yes">Provide restricted gene list</option>
2557 </param>
2558 <when value="no">
2559 <param type="hidden" name="genelist2" value="-1"/>
2560 </when>
2561 <when value="yes">
2562 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2563 </when>
2564 </conditional>
2565 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2566 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2567 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2568 <!-- END: 9 samples, yes refpairs, entry 2-->
2569 <!-- START: 9 samples, yes refpairs, entry 3-->
2570 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2571 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
2572 <conditional name="genelist3">
2573 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2574 <option value="no">Plot whole genome</option>
2575 <option value="yes">Provide restricted gene list</option>
2576 </param>
2577 <when value="no">
2578 <param type="hidden" name="genelist3" value="-1"/>
2579 </when>
2580 <when value="yes">
2581 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2582 </when>
2583 </conditional>
2584 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2585 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2586 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2587 <!-- END: 9 samples, yes refpairs, entry 3-->
2588 <!-- START: 9 samples, yes refpairs, entry 4-->
2589 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2590 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
2591 <conditional name="genelist4">
2592 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2593 <option value="no">Plot whole genome</option>
2594 <option value="yes">Provide restricted gene list</option>
2595 </param>
2596 <when value="no">
2597 <param type="hidden" name="genelist4" value="-1"/>
2598 </when>
2599 <when value="yes">
2600 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2601 </when>
2602 </conditional>
2603 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2604 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2605 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2606 <!-- END: 9 samples, yes refpairs, entry 4-->
2607 <!-- START: 9 samples, yes refpairs, entry 5-->
2608 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2609 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
2610 <conditional name="genelist5">
2611 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2612 <option value="no">Plot whole genome</option>
2613 <option value="yes">Provide restricted gene list</option>
2614 </param>
2615 <when value="no">
2616 <param type="hidden" name="genelist5" value="-1"/>
2617 </when>
2618 <when value="yes">
2619 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2620 </when>
2621 </conditional>
2622 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2623 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2624 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2625 <!-- END: 9 samples, yes refpairs, entry 5-->
2626 <!-- START: 9 samples, yes refpairs, entry 6-->
2627 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2628 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
2629 <conditional name="genelist6">
2630 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2631 <option value="no">Plot whole genome</option>
2632 <option value="yes">Provide restricted gene list</option>
2633 </param>
2634 <when value="no">
2635 <param type="hidden" name="genelist6" value="-1"/>
2636 </when>
2637 <when value="yes">
2638 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2639 </when>
2640 </conditional>
2641 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2642 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2643 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2644 <!-- END: 9 samples, yes refpairs, entry 6-->
2645 <!-- START: 9 samples, yes refpairs, entry 7-->
2646 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2647 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
2648 <conditional name="genelist7">
2649 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2650 <option value="no">Plot whole genome</option>
2651 <option value="yes">Provide restricted gene list</option>
2652 </param>
2653 <when value="no">
2654 <param type="hidden" name="genelist7" value="-1"/>
2655 </when>
2656 <when value="yes">
2657 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2658 </when>
2659 </conditional>
2660 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2661 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2662 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2663 <!-- END: 9 samples, yes refpairs, entry 7-->
2664 <!-- START: 9 samples, yes refpairs, entry 8-->
2665 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2666 <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/>
2667 <conditional name="genelist8">
2668 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2669 <option value="no">Plot whole genome</option>
2670 <option value="yes">Provide restricted gene list</option>
2671 </param>
2672 <when value="no">
2673 <param type="hidden" name="genelist8" value="-1"/>
2674 </when>
2675 <when value="yes">
2676 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2677 </when>
2678 </conditional>
2679 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2680 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2681 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2682 <!-- END: 9 samples, yes refpairs, entry 8-->
2683 <!-- START: 9 samples, yes refpairs, entry 9-->
2684 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
2685 <param type="data" name="reffile9" label="Sample 9: Reference BAM file"/>
2686 <conditional name="genelist9">
2687 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
2688 <option value="no">Plot whole genome</option>
2689 <option value="yes">Provide restricted gene list</option>
2690 </param>
2691 <when value="no">
2692 <param type="hidden" name="genelist9" value="-1"/>
2693 </when>
2694 <when value="yes">
2695 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
2696 </when>
2697 </conditional>
2698 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
2699 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
2700 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
2701 <!-- END: 9 samples, yes refpairs, entry 9-->
2702 </when>
2703 </conditional>
2704 </when>
2705 <when value="10">
2706 <conditional name="usepair">
2707 <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.">
2708 <option value="no">No</option>
2709 <option value="yes">Yes</option>
2710 </param>
2711 <when value="no">
2712 <!-- START: 10 samples, no refpairs, entry 1-->
2713 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2714 <param type="hidden" name="reffile1" value="na"/>
2715 <conditional name="genelist1">
2716 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2717 <option value="no">Plot whole genome</option>
2718 <option value="yes">Provide restricted gene list</option>
2719 </param>
2720 <when value="no">
2721 <param type="hidden" name="genelist1" value="-1"/>
2722 </when>
2723 <when value="yes">
2724 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2725 </when>
2726 </conditional>
2727 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2728 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2729 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2730 <!-- END: 10 samples, no refpairs, entry 1-->
2731 <!-- START: 10 samples, no refpairs, entry 2-->
2732 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2733 <param type="hidden" name="reffile2" value="na"/>
2734 <conditional name="genelist2">
2735 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2736 <option value="no">Plot whole genome</option>
2737 <option value="yes">Provide restricted gene list</option>
2738 </param>
2739 <when value="no">
2740 <param type="hidden" name="genelist2" value="-1"/>
2741 </when>
2742 <when value="yes">
2743 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2744 </when>
2745 </conditional>
2746 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2747 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2748 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2749 <!-- END: 10 samples, no refpairs, entry 2-->
2750 <!-- START: 10 samples, no refpairs, entry 3-->
2751 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2752 <param type="hidden" name="reffile3" value="na"/>
2753 <conditional name="genelist3">
2754 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2755 <option value="no">Plot whole genome</option>
2756 <option value="yes">Provide restricted gene list</option>
2757 </param>
2758 <when value="no">
2759 <param type="hidden" name="genelist3" value="-1"/>
2760 </when>
2761 <when value="yes">
2762 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2763 </when>
2764 </conditional>
2765 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2766 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2767 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2768 <!-- END: 10 samples, no refpairs, entry 3-->
2769 <!-- START: 10 samples, no refpairs, entry 4-->
2770 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2771 <param type="hidden" name="reffile4" value="na"/>
2772 <conditional name="genelist4">
2773 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2774 <option value="no">Plot whole genome</option>
2775 <option value="yes">Provide restricted gene list</option>
2776 </param>
2777 <when value="no">
2778 <param type="hidden" name="genelist4" value="-1"/>
2779 </when>
2780 <when value="yes">
2781 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2782 </when>
2783 </conditional>
2784 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2785 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2786 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2787 <!-- END: 10 samples, no refpairs, entry 4-->
2788 <!-- START: 10 samples, no refpairs, entry 5-->
2789 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2790 <param type="hidden" name="reffile5" value="na"/>
2791 <conditional name="genelist5">
2792 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2793 <option value="no">Plot whole genome</option>
2794 <option value="yes">Provide restricted gene list</option>
2795 </param>
2796 <when value="no">
2797 <param type="hidden" name="genelist5" value="-1"/>
2798 </when>
2799 <when value="yes">
2800 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2801 </when>
2802 </conditional>
2803 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2804 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2805 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2806 <!-- END: 10 samples, no refpairs, entry 5-->
2807 <!-- START: 10 samples, no refpairs, entry 6-->
2808 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2809 <param type="hidden" name="reffile6" value="na"/>
2810 <conditional name="genelist6">
2811 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2812 <option value="no">Plot whole genome</option>
2813 <option value="yes">Provide restricted gene list</option>
2814 </param>
2815 <when value="no">
2816 <param type="hidden" name="genelist6" value="-1"/>
2817 </when>
2818 <when value="yes">
2819 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2820 </when>
2821 </conditional>
2822 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2823 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2824 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2825 <!-- END: 10 samples, no refpairs, entry 6-->
2826 <!-- START: 10 samples, no refpairs, entry 7-->
2827 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2828 <param type="hidden" name="reffile7" value="na"/>
2829 <conditional name="genelist7">
2830 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2831 <option value="no">Plot whole genome</option>
2832 <option value="yes">Provide restricted gene list</option>
2833 </param>
2834 <when value="no">
2835 <param type="hidden" name="genelist7" value="-1"/>
2836 </when>
2837 <when value="yes">
2838 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2839 </when>
2840 </conditional>
2841 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2842 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2843 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2844 <!-- END: 10 samples, no refpairs, entry 7-->
2845 <!-- START: 10 samples, no refpairs, entry 8-->
2846 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2847 <param type="hidden" name="reffile8" value="na"/>
2848 <conditional name="genelist8">
2849 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2850 <option value="no">Plot whole genome</option>
2851 <option value="yes">Provide restricted gene list</option>
2852 </param>
2853 <when value="no">
2854 <param type="hidden" name="genelist8" value="-1"/>
2855 </when>
2856 <when value="yes">
2857 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2858 </when>
2859 </conditional>
2860 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2861 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2862 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2863 <!-- END: 10 samples, no refpairs, entry 8-->
2864 <!-- START: 10 samples, no refpairs, entry 9-->
2865 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
2866 <param type="hidden" name="reffile9" value="na"/>
2867 <conditional name="genelist9">
2868 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
2869 <option value="no">Plot whole genome</option>
2870 <option value="yes">Provide restricted gene list</option>
2871 </param>
2872 <when value="no">
2873 <param type="hidden" name="genelist9" value="-1"/>
2874 </when>
2875 <when value="yes">
2876 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
2877 </when>
2878 </conditional>
2879 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
2880 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
2881 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
2882 <!-- END: 10 samples, no refpairs, entry 9-->
2883 <!-- START: 10 samples, no refpairs, entry 10-->
2884 <param type="data" name="bamfile10" label="Sample 10: Input BAM file"/>
2885 <param type="hidden" name="reffile10" value="na"/>
2886 <conditional name="genelist10">
2887 <param type="select" name="usegenelist10" label="Sample 10: Gene list">
2888 <option value="no">Plot whole genome</option>
2889 <option value="yes">Provide restricted gene list</option>
2890 </param>
2891 <when value="no">
2892 <param type="hidden" name="genelist10" value="-1"/>
2893 </when>
2894 <when value="yes">
2895 <param type="data" name="genelist10" label="Choose the uploaded gene list for plotting"/>
2896 </when>
2897 </conditional>
2898 <param type="text" name="title10" value="plot10" label="Sample 10: Image title"/>
2899 <param type="text" name="fraglen10" value="150" label="Sample 10: Expected fragment length"/>
2900 <param type="text" name="linecol10" value="tan3" label="Sample 10: Line plot color"/>
2901 <!-- END: 10 samples, no refpairs, entry 10-->
2902 </when>
2903 <when value="yes">
2904 <!-- START: 10 samples, yes refpairs, entry 1-->
2905 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2906 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
2907 <conditional name="genelist1">
2908 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2909 <option value="no">Plot whole genome</option>
2910 <option value="yes">Provide restricted gene list</option>
2911 </param>
2912 <when value="no">
2913 <param type="hidden" name="genelist1" value="-1"/>
2914 </when>
2915 <when value="yes">
2916 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2917 </when>
2918 </conditional>
2919 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2920 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2921 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2922 <!-- END: 10 samples, yes refpairs, entry 1-->
2923 <!-- START: 10 samples, yes refpairs, entry 2-->
2924 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2925 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
2926 <conditional name="genelist2">
2927 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2928 <option value="no">Plot whole genome</option>
2929 <option value="yes">Provide restricted gene list</option>
2930 </param>
2931 <when value="no">
2932 <param type="hidden" name="genelist2" value="-1"/>
2933 </when>
2934 <when value="yes">
2935 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2936 </when>
2937 </conditional>
2938 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2939 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2940 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2941 <!-- END: 10 samples, yes refpairs, entry 2-->
2942 <!-- START: 10 samples, yes refpairs, entry 3-->
2943 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2944 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
2945 <conditional name="genelist3">
2946 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2947 <option value="no">Plot whole genome</option>
2948 <option value="yes">Provide restricted gene list</option>
2949 </param>
2950 <when value="no">
2951 <param type="hidden" name="genelist3" value="-1"/>
2952 </when>
2953 <when value="yes">
2954 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2955 </when>
2956 </conditional>
2957 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2958 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2959 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2960 <!-- END: 10 samples, yes refpairs, entry 3-->
2961 <!-- START: 10 samples, yes refpairs, entry 4-->
2962 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2963 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
2964 <conditional name="genelist4">
2965 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2966 <option value="no">Plot whole genome</option>
2967 <option value="yes">Provide restricted gene list</option>
2968 </param>
2969 <when value="no">
2970 <param type="hidden" name="genelist4" value="-1"/>
2971 </when>
2972 <when value="yes">
2973 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2974 </when>
2975 </conditional>
2976 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2977 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2978 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2979 <!-- END: 10 samples, yes refpairs, entry 4-->
2980 <!-- START: 10 samples, yes refpairs, entry 5-->
2981 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2982 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
2983 <conditional name="genelist5">
2984 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2985 <option value="no">Plot whole genome</option>
2986 <option value="yes">Provide restricted gene list</option>
2987 </param>
2988 <when value="no">
2989 <param type="hidden" name="genelist5" value="-1"/>
2990 </when>
2991 <when value="yes">
2992 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2993 </when>
2994 </conditional>
2995 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2996 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2997 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2998 <!-- END: 10 samples, yes refpairs, entry 5-->
2999 <!-- START: 10 samples, yes refpairs, entry 6-->
3000 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
3001 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
3002 <conditional name="genelist6">
3003 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
3004 <option value="no">Plot whole genome</option>
3005 <option value="yes">Provide restricted gene list</option>
3006 </param>
3007 <when value="no">
3008 <param type="hidden" name="genelist6" value="-1"/>
3009 </when>
3010 <when value="yes">
3011 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
3012 </when>
3013 </conditional>
3014 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
3015 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
3016 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
3017 <!-- END: 10 samples, yes refpairs, entry 6-->
3018 <!-- START: 10 samples, yes refpairs, entry 7-->
3019 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
3020 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
3021 <conditional name="genelist7">
3022 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
3023 <option value="no">Plot whole genome</option>
3024 <option value="yes">Provide restricted gene list</option>
3025 </param>
3026 <when value="no">
3027 <param type="hidden" name="genelist7" value="-1"/>
3028 </when>
3029 <when value="yes">
3030 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
3031 </when>
3032 </conditional>
3033 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
3034 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
3035 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
3036 <!-- END: 10 samples, yes refpairs, entry 7-->
3037 <!-- START: 10 samples, yes refpairs, entry 8-->
3038 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
3039 <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/>
3040 <conditional name="genelist8">
3041 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
3042 <option value="no">Plot whole genome</option>
3043 <option value="yes">Provide restricted gene list</option>
3044 </param>
3045 <when value="no">
3046 <param type="hidden" name="genelist8" value="-1"/>
3047 </when>
3048 <when value="yes">
3049 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
3050 </when>
3051 </conditional>
3052 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
3053 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
3054 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
3055 <!-- END: 10 samples, yes refpairs, entry 8-->
3056 <!-- START: 10 samples, yes refpairs, entry 9-->
3057 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
3058 <param type="data" name="reffile9" label="Sample 9: Reference BAM file"/>
3059 <conditional name="genelist9">
3060 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
3061 <option value="no">Plot whole genome</option>
3062 <option value="yes">Provide restricted gene list</option>
3063 </param>
3064 <when value="no">
3065 <param type="hidden" name="genelist9" value="-1"/>
3066 </when>
3067 <when value="yes">
3068 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
3069 </when>
3070 </conditional>
3071 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
3072 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
3073 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
3074 <!-- END: 10 samples, yes refpairs, entry 9-->
3075 <!-- START: 10 samples, yes refpairs, entry 10-->
3076 <param type="data" name="bamfile10" label="Sample 10: Input BAM file"/>
3077 <param type="data" name="reffile10" label="Sample 10: Reference BAM file"/>
3078 <conditional name="genelist10">
3079 <param type="select" name="usegenelist10" label="Sample 10: Gene list">
3080 <option value="no">Plot whole genome</option>
3081 <option value="yes">Provide restricted gene list</option>
3082 </param>
3083 <when value="no">
3084 <param type="hidden" name="genelist10" value="-1"/>
3085 </when>
3086 <when value="yes">
3087 <param type="data" name="genelist10" label="Choose the uploaded gene list for plotting"/>
3088 </when>
3089 </conditional>
3090 <param type="text" name="title10" value="plot10" label="Sample 10: Image title"/>
3091 <param type="text" name="fraglen10" value="150" label="Sample 10: Expected fragment length"/>
3092 <param type="text" name="linecol10" value="tan3" label="Sample 10: Line plot color"/>
3093 <!-- END: 10 samples, yes refpairs, entry 10-->
3094 </when>
3095 </conditional>
3096 </when>
3097 </conditional>
3098
3099
3100
3101 <param type="select" name="gene_database" label="Supported gene database: RefSeq, Ensembl">
3102 <option value="ensembl">Ensembl</option>
3103 <option value="refseq">RefSeq</option>
3104 </param>
3105 <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."/>
3106 <conditional name="GO">
3107 <param type="select" name="gene_order" label="Gene order algorithm">
3108 <option value="total">Overall enrichment of the 1st profile</option>
3109 <option value="hc">Hierarchical clustering</option>
3110 <option value="max">Peak value of the 1st profile</option>
3111 <option value="prod">Product of all profiles on the same region</option>
3112 <option value="diff">Difference between the 1st and 2nd profiles</option>
3113 <option value="km">K-means clustering</option>
3114 <option value="none">No ranking algorithm applied. Use order in gene list.</option>
3115 </param>
3116 <when value="km">
3117 <param type="text" name="KNC" value="5" label="K-means: Number of clusters" help=""/>
3118 <param type="text" name="MIT" value="20" label="K-means: Number of iterations" help=""/>
3119 <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."/>
3120 </when>
3121 <when value="total">
3122 <param type="hidden" name="KNC" value="NA" />
3123 <param type="hidden" name="MIT" value="NA" />
3124 <param type="hidden" name="NRS" value="NA" />
3125 </when>
3126 <when value="hc">
3127 <param type="hidden" name="KNC" value="NA" />
3128 <param type="hidden" name="MIT" value="NA" />
3129 <param type="hidden" name="NRS" value="NA" />
3130 </when>
3131 <when value="max">
3132 <param type="hidden" name="KNC" value="NA" />
3133 <param type="hidden" name="MIT" value="NA" />
3134 <param type="hidden" name="NRS" value="NA" />
3135 </when>
3136 <when value="prod">
3137 <param type="hidden" name="KNC" value="NA" />
3138 <param type="hidden" name="MIT" value="NA" />
3139 <param type="hidden" name="NRS" value="NA" />
3140 </when>
3141 <when value="diff">
3142 <param type="hidden" name="KNC" value="NA" />
3143 <param type="hidden" name="MIT" value="NA" />
3144 <param type="hidden" name="NRS" value="NA" />
3145 </when>
3146 <when value="none">
3147 <param type="hidden" name="KNC" value="NA" />
3148 <param type="hidden" name="MIT" value="NA" />
3149 <param type="hidden" name="NRS" value="NA" />
3150 </when>
3151 </conditional>
3152 <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."/>
3153 <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%."/>
3154 <param type="select" name="standard_error" label="Plot standard errors" help="Standard errors will be rendered as shaded area around each curve.">
3155 <option value="1">Yes</option>
3156 <option value="0">No</option>
3157 </param>
3158
3159 <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."/>
3160 <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."/>
3161 <param type="select" name="smooth_method" label="Moving window width to smooth avg. profiles">
3162 <option value="1">No</option>
3163 <option value="3">Slightly</option>
3164 <option value="5">Somewhat</option>
3165 <option value="9">Quite</option>
3166 <option value="13">Super</option>
3167 </param>
3168 <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."/>
3169 <!--
3170 -->
3171 </inputs>
3172
3173 <help>---TEST---</help>
3174 <outputs>
3175 <data format="pdf" name="out_avg_png" />
3176 <data format="pdf" name="out_hm_png" />
3177 <data format="zip" name="out_zip"/>
3178 </outputs>
3179 </tool>