Mercurial > repos > ngsplot > ngsplot

comparison ngsplot_galaxytoolshed_v.10/ngsplot_main/ngsplot.xml @ 12:f7debdafc7cb draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author ngsplot
date Tue, 31 Mar 2015 10:15:27 -0400
parents
children
comparison
equal deleted inserted replaced
11:896dfca167fb 12:f7debdafc7cb
1 <tool id="ngs.plot" name="ngs.plot">
2
3 <command interpreter="perl">
4 #if $numsamples.numsamples2 == "1":
5 runNGSplot.pl
6 $genome_name
7 $genomic_region_source_type.genomic_region
8 $genomic_region_source_type.further_information
9 $genomic_region_source_type.interval_size
10 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
11 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
12 $numsamples.numsamples2
13 $numsamples.usepair.usepair1
14
15 $numsamples.usepair.bamfile1
16 $numsamples.usepair.reffile1
17 $numsamples.usepair.genelist1.usegenelist1
18 $numsamples.usepair.genelist1.genelist1
19 $numsamples.usepair.title1
20 $numsamples.usepair.fraglen1
21 $numsamples.usepair.linecol1
22
23 $gene_database
24 $randomly_sample
25 $GO.gene_order
26 $GO.KNC
27 $GO.MIT
28 $GO.NRS
29 $chunk_size
30 $quality_requirement
31 $standard_error
32 $radius_size
33 $flooding_fraction
34 $smooth_method
35 $shaded_area
36 $out_zip $out_avg_png $out_hm_png
37
38 #else if $numsamples.numsamples2 == "2":
39 runNGSplot.pl
40 $genome_name
41 $genomic_region_source_type.genomic_region
42 $genomic_region_source_type.further_information
43 $genomic_region_source_type.interval_size
44 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
45 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
46 $numsamples.numsamples2
47 $numsamples.usepair.usepair1
48
49 $numsamples.usepair.bamfile1
50 $numsamples.usepair.reffile1
51 $numsamples.usepair.genelist1.usegenelist1
52 $numsamples.usepair.genelist1.genelist1
53 $numsamples.usepair.title1
54 $numsamples.usepair.fraglen1
55 $numsamples.usepair.linecol1
56
57 $numsamples.usepair.bamfile2
58 $numsamples.usepair.reffile2
59 $numsamples.usepair.genelist2.usegenelist2
60 $numsamples.usepair.genelist2.genelist2
61 $numsamples.usepair.title2
62 $numsamples.usepair.fraglen2
63 $numsamples.usepair.linecol2
64
65 $gene_database
66 $randomly_sample
67 $GO.gene_order
68 $GO.KNC
69 $GO.MIT
70 $GO.NRS
71 $chunk_size
72 $quality_requirement
73 $standard_error
74 $radius_size
75 $flooding_fraction
76 $smooth_method
77 $shaded_area
78 $out_zip $out_avg_png $out_hm_png
79
80 #else if $numsamples.numsamples2 == "3":
81 runNGSplot.pl
82 $genome_name
83 $genomic_region_source_type.genomic_region
84 $genomic_region_source_type.further_information
85 $genomic_region_source_type.interval_size
86 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
87 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
88 $numsamples.numsamples2
89 $numsamples.usepair.usepair1
90
91 $numsamples.usepair.bamfile1
92 $numsamples.usepair.reffile1
93 $numsamples.usepair.genelist1.usegenelist1
94 $numsamples.usepair.genelist1.genelist1
95 $numsamples.usepair.title1
96 $numsamples.usepair.fraglen1
97 $numsamples.usepair.linecol1
98
99 $numsamples.usepair.bamfile2
100 $numsamples.usepair.reffile2
101 $numsamples.usepair.genelist2.usegenelist2
102 $numsamples.usepair.genelist2.genelist2
103 $numsamples.usepair.title2
104 $numsamples.usepair.fraglen2
105 $numsamples.usepair.linecol2
106
107 $numsamples.usepair.bamfile3
108 $numsamples.usepair.reffile3
109 $numsamples.usepair.genelist3.usegenelist3
110 $numsamples.usepair.genelist3.genelist3
111 $numsamples.usepair.title3
112 $numsamples.usepair.fraglen3
113 $numsamples.usepair.linecol3
114
115 $gene_database
116 $randomly_sample
117 $GO.gene_order
118 $GO.KNC
119 $GO.MIT
120 $GO.NRS
121 $chunk_size
122 $quality_requirement
123 $standard_error
124 $radius_size
125 $flooding_fraction
126 $smooth_method
127 $shaded_area
128 $out_zip $out_avg_png $out_hm_png
129
130 #else if $numsamples.numsamples2 == "4":
131 runNGSplot.pl
132 $genome_name
133 $genomic_region_source_type.genomic_region
134 $genomic_region_source_type.further_information
135 $genomic_region_source_type.interval_size
136 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
137 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
138 $numsamples.numsamples2
139 $numsamples.usepair.usepair1
140
141 $numsamples.usepair.bamfile1
142 $numsamples.usepair.reffile1
143 $numsamples.usepair.genelist1.usegenelist1
144 $numsamples.usepair.genelist1.genelist1
145 $numsamples.usepair.title1
146 $numsamples.usepair.fraglen1
147 $numsamples.usepair.linecol1
148
149 $numsamples.usepair.bamfile2
150 $numsamples.usepair.reffile2
151 $numsamples.usepair.genelist2.usegenelist2
152 $numsamples.usepair.genelist2.genelist2
153 $numsamples.usepair.title2
154 $numsamples.usepair.fraglen2
155 $numsamples.usepair.linecol2
156
157 $numsamples.usepair.bamfile3
158 $numsamples.usepair.reffile3
159 $numsamples.usepair.genelist3.usegenelist3
160 $numsamples.usepair.genelist3.genelist3
161 $numsamples.usepair.title3
162 $numsamples.usepair.fraglen3
163 $numsamples.usepair.linecol3
164
165 $numsamples.usepair.bamfile4
166 $numsamples.usepair.reffile4
167 $numsamples.usepair.genelist4.usegenelist4
168 $numsamples.usepair.genelist4.genelist4
169 $numsamples.usepair.title4
170 $numsamples.usepair.fraglen4
171 $numsamples.usepair.linecol4
172
173 $gene_database
174 $randomly_sample
175 $GO.gene_order
176 $GO.KNC
177 $GO.MIT
178 $GO.NRS
179 $chunk_size
180 $quality_requirement
181 $standard_error
182 $radius_size
183 $flooding_fraction
184 $smooth_method
185 $shaded_area
186 $out_zip $out_avg_png $out_hm_png
187
188 #else if $numsamples.numsamples2 == "5":
189 runNGSplot.pl
190 $genome_name
191 $genomic_region_source_type.genomic_region
192 $genomic_region_source_type.further_information
193 $genomic_region_source_type.interval_size
194 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
195 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
196 $numsamples.numsamples2
197 $numsamples.usepair.usepair1
198
199 $numsamples.usepair.bamfile1
200 $numsamples.usepair.reffile1
201 $numsamples.usepair.genelist1.usegenelist1
202 $numsamples.usepair.genelist1.genelist1
203 $numsamples.usepair.title1
204 $numsamples.usepair.fraglen1
205 $numsamples.usepair.linecol1
206
207 $numsamples.usepair.bamfile2
208 $numsamples.usepair.reffile2
209 $numsamples.usepair.genelist2.usegenelist2
210 $numsamples.usepair.genelist2.genelist2
211 $numsamples.usepair.title2
212 $numsamples.usepair.fraglen2
213 $numsamples.usepair.linecol2
214
215 $numsamples.usepair.bamfile3
216 $numsamples.usepair.reffile3
217 $numsamples.usepair.genelist3.usegenelist3
218 $numsamples.usepair.genelist3.genelist3
219 $numsamples.usepair.title3
220 $numsamples.usepair.fraglen3
221 $numsamples.usepair.linecol3
222
223 $numsamples.usepair.bamfile4
224 $numsamples.usepair.reffile4
225 $numsamples.usepair.genelist4.usegenelist4
226 $numsamples.usepair.genelist4.genelist4
227 $numsamples.usepair.title4
228 $numsamples.usepair.fraglen4
229 $numsamples.usepair.linecol4
230
231 $numsamples.usepair.bamfile5
232 $numsamples.usepair.reffile5
233 $numsamples.usepair.genelist5.usegenelist5
234 $numsamples.usepair.genelist5.genelist5
235 $numsamples.usepair.title5
236 $numsamples.usepair.fraglen5
237 $numsamples.usepair.linecol5
238
239 $gene_database
240 $randomly_sample
241 $GO.gene_order
242 $GO.KNC
243 $GO.MIT
244 $GO.NRS
245 $chunk_size
246 $quality_requirement
247 $standard_error
248 $radius_size
249 $flooding_fraction
250 $smooth_method
251 $shaded_area
252 $out_zip $out_avg_png $out_hm_png
253
254 #else if $numsamples.numsamples2 == "6":
255 runNGSplot.pl
256 $genome_name
257 $genomic_region_source_type.genomic_region
258 $genomic_region_source_type.further_information
259 $genomic_region_source_type.interval_size
260 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
261 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
262 $numsamples.numsamples2
263 $numsamples.usepair.usepair1
264
265 $numsamples.usepair.bamfile1
266 $numsamples.usepair.reffile1
267 $numsamples.usepair.genelist1.usegenelist1
268 $numsamples.usepair.genelist1.genelist1
269 $numsamples.usepair.title1
270 $numsamples.usepair.fraglen1
271 $numsamples.usepair.linecol1
272
273 $numsamples.usepair.bamfile2
274 $numsamples.usepair.reffile2
275 $numsamples.usepair.genelist2.usegenelist2
276 $numsamples.usepair.genelist2.genelist2
277 $numsamples.usepair.title2
278 $numsamples.usepair.fraglen2
279 $numsamples.usepair.linecol2
280
281 $numsamples.usepair.bamfile3
282 $numsamples.usepair.reffile3
283 $numsamples.usepair.genelist3.usegenelist3
284 $numsamples.usepair.genelist3.genelist3
285 $numsamples.usepair.title3
286 $numsamples.usepair.fraglen3
287 $numsamples.usepair.linecol3
288
289 $numsamples.usepair.bamfile4
290 $numsamples.usepair.reffile4
291 $numsamples.usepair.genelist4.usegenelist4
292 $numsamples.usepair.genelist4.genelist4
293 $numsamples.usepair.title4
294 $numsamples.usepair.fraglen4
295 $numsamples.usepair.linecol4
296
297 $numsamples.usepair.bamfile5
298 $numsamples.usepair.reffile5
299 $numsamples.usepair.genelist5.usegenelist5
300 $numsamples.usepair.genelist5.genelist5
301 $numsamples.usepair.title5
302 $numsamples.usepair.fraglen5
303 $numsamples.usepair.linecol5
304
305 $numsamples.usepair.bamfile6
306 $numsamples.usepair.reffile6
307 $numsamples.usepair.genelist6.usegenelist6
308 $numsamples.usepair.genelist6.genelist6
309 $numsamples.usepair.title6
310 $numsamples.usepair.fraglen6
311 $numsamples.usepair.linecol6
312
313 $gene_database
314 $randomly_sample
315 $GO.gene_order
316 $GO.KNC
317 $GO.MIT
318 $GO.NRS
319 $chunk_size
320 $quality_requirement
321 $standard_error
322 $radius_size
323 $flooding_fraction
324 $smooth_method
325 $shaded_area
326 $out_zip $out_avg_png $out_hm_png
327
328 #else if $numsamples.numsamples2 == "7":
329 runNGSplot.pl
330 $genome_name
331 $genomic_region_source_type.genomic_region
332 $genomic_region_source_type.further_information
333 $genomic_region_source_type.interval_size
334 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
335 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
336 $numsamples.numsamples2
337 $numsamples.usepair.usepair1
338
339 $numsamples.usepair.bamfile1
340 $numsamples.usepair.reffile1
341 $numsamples.usepair.genelist1.usegenelist1
342 $numsamples.usepair.genelist1.genelist1
343 $numsamples.usepair.title1
344 $numsamples.usepair.fraglen1
345 $numsamples.usepair.linecol1
346
347 $numsamples.usepair.bamfile2
348 $numsamples.usepair.reffile2
349 $numsamples.usepair.genelist2.usegenelist2
350 $numsamples.usepair.genelist2.genelist2
351 $numsamples.usepair.title2
352 $numsamples.usepair.fraglen2
353 $numsamples.usepair.linecol2
354
355 $numsamples.usepair.bamfile3
356 $numsamples.usepair.reffile3
357 $numsamples.usepair.genelist3.usegenelist3
358 $numsamples.usepair.genelist3.genelist3
359 $numsamples.usepair.title3
360 $numsamples.usepair.fraglen3
361 $numsamples.usepair.linecol3
362
363 $numsamples.usepair.bamfile4
364 $numsamples.usepair.reffile4
365 $numsamples.usepair.genelist4.usegenelist4
366 $numsamples.usepair.genelist4.genelist4
367 $numsamples.usepair.title4
368 $numsamples.usepair.fraglen4
369 $numsamples.usepair.linecol4
370
371 $numsamples.usepair.bamfile5
372 $numsamples.usepair.reffile5
373 $numsamples.usepair.genelist5.usegenelist5
374 $numsamples.usepair.genelist5.genelist5
375 $numsamples.usepair.title5
376 $numsamples.usepair.fraglen5
377 $numsamples.usepair.linecol5
378
379 $numsamples.usepair.bamfile6
380 $numsamples.usepair.reffile6
381 $numsamples.usepair.genelist6.usegenelist6
382 $numsamples.usepair.genelist6.genelist6
383 $numsamples.usepair.title6
384 $numsamples.usepair.fraglen6
385 $numsamples.usepair.linecol6
386
387 $numsamples.usepair.bamfile7
388 $numsamples.usepair.reffile7
389 $numsamples.usepair.genelist7.usegenelist7
390 $numsamples.usepair.genelist7.genelist7
391 $numsamples.usepair.title7
392 $numsamples.usepair.fraglen7
393 $numsamples.usepair.linecol7
394
395 $gene_database
396 $randomly_sample
397 $GO.gene_order
398 $GO.KNC
399 $GO.MIT
400 $GO.NRS
401 $chunk_size
402 $quality_requirement
403 $standard_error
404 $radius_size
405 $flooding_fraction
406 $smooth_method
407 $shaded_area
408 $out_zip $out_avg_png $out_hm_png
409
410 #else if $numsamples.numsamples2 == "8":
411 runNGSplot.pl
412 $genome_name
413 $genomic_region_source_type.genomic_region
414 $genomic_region_source_type.further_information
415 $genomic_region_source_type.interval_size
416 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
417 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
418 $numsamples.numsamples2
419 $numsamples.usepair.usepair1
420
421 $numsamples.usepair.bamfile1
422 $numsamples.usepair.reffile1
423 $numsamples.usepair.genelist1.usegenelist1
424 $numsamples.usepair.genelist1.genelist1
425 $numsamples.usepair.title1
426 $numsamples.usepair.fraglen1
427 $numsamples.usepair.linecol1
428
429 $numsamples.usepair.bamfile2
430 $numsamples.usepair.reffile2
431 $numsamples.usepair.genelist2.usegenelist2
432 $numsamples.usepair.genelist2.genelist2
433 $numsamples.usepair.title2
434 $numsamples.usepair.fraglen2
435 $numsamples.usepair.linecol2
436
437 $numsamples.usepair.bamfile3
438 $numsamples.usepair.reffile3
439 $numsamples.usepair.genelist3.usegenelist3
440 $numsamples.usepair.genelist3.genelist3
441 $numsamples.usepair.title3
442 $numsamples.usepair.fraglen3
443 $numsamples.usepair.linecol3
444
445 $numsamples.usepair.bamfile4
446 $numsamples.usepair.reffile4
447 $numsamples.usepair.genelist4.usegenelist4
448 $numsamples.usepair.genelist4.genelist4
449 $numsamples.usepair.title4
450 $numsamples.usepair.fraglen4
451 $numsamples.usepair.linecol4
452
453 $numsamples.usepair.bamfile5
454 $numsamples.usepair.reffile5
455 $numsamples.usepair.genelist5.usegenelist5
456 $numsamples.usepair.genelist5.genelist5
457 $numsamples.usepair.title5
458 $numsamples.usepair.fraglen5
459 $numsamples.usepair.linecol5
460
461 $numsamples.usepair.bamfile6
462 $numsamples.usepair.reffile6
463 $numsamples.usepair.genelist6.usegenelist6
464 $numsamples.usepair.genelist6.genelist6
465 $numsamples.usepair.title6
466 $numsamples.usepair.fraglen6
467 $numsamples.usepair.linecol6
468
469 $numsamples.usepair.bamfile7
470 $numsamples.usepair.reffile7
471 $numsamples.usepair.genelist7.usegenelist7
472 $numsamples.usepair.genelist7.genelist7
473 $numsamples.usepair.title7
474 $numsamples.usepair.fraglen7
475 $numsamples.usepair.linecol7
476
477 $numsamples.usepair.bamfile8
478 $numsamples.usepair.reffile8
479 $numsamples.usepair.genelist8.usegenelist8
480 $numsamples.usepair.genelist8.genelist8
481 $numsamples.usepair.title8
482 $numsamples.usepair.fraglen8
483 $numsamples.usepair.linecol8
484
485 $gene_database
486 $randomly_sample
487 $GO.gene_order
488 $GO.KNC
489 $GO.MIT
490 $GO.NRS
491 $chunk_size
492 $quality_requirement
493 $standard_error
494 $radius_size
495 $flooding_fraction
496 $smooth_method
497 $shaded_area
498 $out_zip $out_avg_png $out_hm_png
499
500 #else if $numsamples.numsamples2 == "9":
501 runNGSplot.pl
502 $genome_name
503 $genomic_region_source_type.genomic_region
504 $genomic_region_source_type.further_information
505 $genomic_region_source_type.interval_size
506 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
507 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
508 $numsamples.numsamples2
509 $numsamples.usepair.usepair1
510
511 $numsamples.usepair.bamfile1
512 $numsamples.usepair.reffile1
513 $numsamples.usepair.genelist1.usegenelist1
514 $numsamples.usepair.genelist1.genelist1
515 $numsamples.usepair.title1
516 $numsamples.usepair.fraglen1
517 $numsamples.usepair.linecol1
518
519 $numsamples.usepair.bamfile2
520 $numsamples.usepair.reffile2
521 $numsamples.usepair.genelist2.usegenelist2
522 $numsamples.usepair.genelist2.genelist2
523 $numsamples.usepair.title2
524 $numsamples.usepair.fraglen2
525 $numsamples.usepair.linecol2
526
527 $numsamples.usepair.bamfile3
528 $numsamples.usepair.reffile3
529 $numsamples.usepair.genelist3.usegenelist3
530 $numsamples.usepair.genelist3.genelist3
531 $numsamples.usepair.title3
532 $numsamples.usepair.fraglen3
533 $numsamples.usepair.linecol3
534
535 $numsamples.usepair.bamfile4
536 $numsamples.usepair.reffile4
537 $numsamples.usepair.genelist4.usegenelist4
538 $numsamples.usepair.genelist4.genelist4
539 $numsamples.usepair.title4
540 $numsamples.usepair.fraglen4
541 $numsamples.usepair.linecol4
542
543 $numsamples.usepair.bamfile5
544 $numsamples.usepair.reffile5
545 $numsamples.usepair.genelist5.usegenelist5
546 $numsamples.usepair.genelist5.genelist5
547 $numsamples.usepair.title5
548 $numsamples.usepair.fraglen5
549 $numsamples.usepair.linecol5
550
551 $numsamples.usepair.bamfile6
552 $numsamples.usepair.reffile6
553 $numsamples.usepair.genelist6.usegenelist6
554 $numsamples.usepair.genelist6.genelist6
555 $numsamples.usepair.title6
556 $numsamples.usepair.fraglen6
557 $numsamples.usepair.linecol6
558
559 $numsamples.usepair.bamfile7
560 $numsamples.usepair.reffile7
561 $numsamples.usepair.genelist7.usegenelist7
562 $numsamples.usepair.genelist7.genelist7
563 $numsamples.usepair.title7
564 $numsamples.usepair.fraglen7
565 $numsamples.usepair.linecol7
566
567 $numsamples.usepair.bamfile8
568 $numsamples.usepair.reffile8
569 $numsamples.usepair.genelist8.usegenelist8
570 $numsamples.usepair.genelist8.genelist8
571 $numsamples.usepair.title8
572 $numsamples.usepair.fraglen8
573 $numsamples.usepair.linecol8
574
575 $numsamples.usepair.bamfile9
576 $numsamples.usepair.reffile9
577 $numsamples.usepair.genelist9.usegenelist9
578 $numsamples.usepair.genelist9.genelist9
579 $numsamples.usepair.title9
580 $numsamples.usepair.fraglen9
581 $numsamples.usepair.linecol9
582
583 $gene_database
584 $randomly_sample
585 $GO.gene_order
586 $GO.KNC
587 $GO.MIT
588 $GO.NRS
589 $chunk_size
590 $quality_requirement
591 $standard_error
592 $radius_size
593 $flooding_fraction
594 $smooth_method
595 $shaded_area
596 $out_zip $out_avg_png $out_hm_png
597
598 #else if $numsamples.numsamples2 == "10":
599 runNGSplot.pl
600 $genome_name
601 $genomic_region_source_type.genomic_region
602 $genomic_region_source_type.further_information
603 $genomic_region_source_type.interval_size
604 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
605 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
606 $numsamples.numsamples2
607 $numsamples.usepair.usepair1
608
609 $numsamples.usepair.bamfile1
610 $numsamples.usepair.reffile1
611 $numsamples.usepair.genelist1.usegenelist1
612 $numsamples.usepair.genelist1.genelist1
613 $numsamples.usepair.title1
614 $numsamples.usepair.fraglen1
615 $numsamples.usepair.linecol1
616
617 $numsamples.usepair.bamfile2
618 $numsamples.usepair.reffile2
619 $numsamples.usepair.genelist2.usegenelist2
620 $numsamples.usepair.genelist2.genelist2
621 $numsamples.usepair.title2
622 $numsamples.usepair.fraglen2
623 $numsamples.usepair.linecol2
624
625 $numsamples.usepair.bamfile3
626 $numsamples.usepair.reffile3
627 $numsamples.usepair.genelist3.usegenelist3
628 $numsamples.usepair.genelist3.genelist3
629 $numsamples.usepair.title3
630 $numsamples.usepair.fraglen3
631 $numsamples.usepair.linecol3
632
633 $numsamples.usepair.bamfile4
634 $numsamples.usepair.reffile4
635 $numsamples.usepair.genelist4.usegenelist4
636 $numsamples.usepair.genelist4.genelist4
637 $numsamples.usepair.title4
638 $numsamples.usepair.fraglen4
639 $numsamples.usepair.linecol4
640
641 $numsamples.usepair.bamfile5
642 $numsamples.usepair.reffile5
643 $numsamples.usepair.genelist5.usegenelist5
644 $numsamples.usepair.genelist5.genelist5
645 $numsamples.usepair.title5
646 $numsamples.usepair.fraglen5
647 $numsamples.usepair.linecol5
648
649 $numsamples.usepair.bamfile6
650 $numsamples.usepair.reffile6
651 $numsamples.usepair.genelist6.usegenelist6
652 $numsamples.usepair.genelist6.genelist6
653 $numsamples.usepair.title6
654 $numsamples.usepair.fraglen6
655 $numsamples.usepair.linecol6
656
657 $numsamples.usepair.bamfile7
658 $numsamples.usepair.reffile7
659 $numsamples.usepair.genelist7.usegenelist7
660 $numsamples.usepair.genelist7.genelist7
661 $numsamples.usepair.title7
662 $numsamples.usepair.fraglen7
663 $numsamples.usepair.linecol7
664
665 $numsamples.usepair.bamfile8
666 $numsamples.usepair.reffile8
667 $numsamples.usepair.genelist8.usegenelist8
668 $numsamples.usepair.genelist8.genelist8
669 $numsamples.usepair.title8
670 $numsamples.usepair.fraglen8
671 $numsamples.usepair.linecol8
672
673 $numsamples.usepair.bamfile9
674 $numsamples.usepair.reffile9
675 $numsamples.usepair.genelist9.usegenelist9
676 $numsamples.usepair.genelist9.genelist9
677 $numsamples.usepair.title9
678 $numsamples.usepair.fraglen9
679 $numsamples.usepair.linecol9
680
681 $numsamples.usepair.bamfile10
682 $numsamples.usepair.reffile10
683 $numsamples.usepair.genelist10.usegenelist10
684 $numsamples.usepair.genelist10.genelist10
685 $numsamples.usepair.title10
686 $numsamples.usepair.fraglen10
687 $numsamples.usepair.linecol10
688
689 $gene_database
690 $randomly_sample
691 $GO.gene_order
692 $GO.KNC
693 $GO.MIT
694 $GO.NRS
695 $chunk_size
696 $quality_requirement
697 $standard_error
698 $radius_size
699 $flooding_fraction
700 $smooth_method
701 $shaded_area
702 $out_zip $out_avg_png $out_hm_png
703
704 #end if:
705
706 </command>
707
708 <!-->
709 <-->
710
711 <inputs>
712 <param type="text" value="mm9" name="genome_name" label="Genome" help="(hg19, mm9, rn4, or other genomes supported by your NGS.plot installation)" >
713 </param>
714 <conditional name="genomic_region_source_type">
715 <param type="select" name="genomic_region" label="Genomic region" help="">
716 <option value="tss">TSS</option>
717 <option value="tes">TES</option>
718 <option value="genebody">Genebody</option>
719 <option value="exon">Exon</option>
720 <option value="cgi">CGI</option>
721 <option value="bed">Customized bed file</option>
722 </param>
723
724 <when value="tss">
725 <param type="select" name="further_information" label="Further information: Not required for TSS">
726 <option value="na">Not Required</option>
727 </param>
728 <param name="interval_size" type="select" label="Interval Region Size: Not required for TSS">
729 <option value="na">Not Required</option>
730 </param>
731 <conditional name="flanking_region_option_source_type">
732 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
733 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
734 <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option-->
735 </param>
736 <when value="flanking_region_size">
737 <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"/>
738 </when>
739 <!--when value="flanking_floating_size">
740 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
741 </when-->
742 </conditional>
743 </when>
744 <when value="tes">
745 <param type="select" name="further_information" label="Further information: Not required for TES">
746 <option value="na">Not Required</option>
747 </param>
748 <param name="interval_size" type="select" label="Interval Region Size: Not required for TES">
749 <option value="na">Not Required</option>
750 </param>
751 <conditional name="flanking_region_option_source_type">
752 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
753 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
754 <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option-->
755 </param>
756 <when value="flanking_region_size">
757 <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"/>
758 </when>
759 <!--when value="flanking_floating_size">
760 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
761 </when-->
762 </conditional>
763 </when>
764 <when value="genebody">
765 <param type="select" name="further_information" label="You selected Genebody, further information can be provided for specific regions to plot">
766 <option value="chipseq">ChIP-seq</option>
767 <option value="rnaseq">RNA-seq</option>
768 </param>
769 <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.">
770 <option value="automatic">Default</option>
771 <option value="0">Small</option>
772 <option value="1">Large</option>
773 </param>
774 <conditional name="flanking_region_option_source_type">
775 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
776 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
777 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
778 </param>
779 <when value="flanking_region_size">
780 <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"/>
781 </when>
782 <when value="flanking_floating_size">
783 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
784 </when>
785 </conditional>
786 </when>
787 <when value="exon">
788 <param type="select" name="further_information" label="You selected Exon, further information can be provided for specific regions to plot">
789 <option value="canonical">Canonical</option>
790 <option value="variant">Variant</option>
791 <option value="promoter">Promoter</option>
792 <option value="polyA">polyA</option>
793 <option value="altAcceptor">altAcceptor</option>
794 <option value="altDonor">altDonor</option>
795 <option value="altBoth">altBoth</option>
796 </param>
797 <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.">
798 <option value="automatic">Default</option>
799 <option value="0">Small</option>
800 <option value="1">Large</option>
801 </param>
802 <conditional name="flanking_region_option_source_type">
803 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
804 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
805 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
806 </param>
807 <when value="flanking_region_size">
808 <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"/>
809 </when>
810 <when value="flanking_floating_size">
811 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
812 </when>
813 </conditional>
814 </when>
815 <when value="cgi">
816 <param type="select" name="further_information" label="You select CGI, further information can be provided for specific regions to plot">
817 <option value="ProximalPromoter">ProximalPromoter</option>
818 <option value="Genebody">GeneBody</option>
819 <option value="Genedesert">GeneDesert</option>
820 <option value="OtherIntergenic">OtherIntergenic</option>
821 <option value="Pericentromere">Pericentromere</option>
822 <option value="Subtelomere">Subtelomere</option>
823 <option value="Promoter1k">Promoter1k</option>
824 <option value="Promoter3k">Promoter3k</option>
825 </param>
826 <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.">
827 <option value="automatic">Default</option>
828 <option value="0">Small</option>
829 <option value="1">Large</option>
830 </param>
831 <conditional name="flanking_region_option_source_type">
832 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
833 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
834 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
835 </param>
836 <when value="flanking_region_size">
837 <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"/>
838 </when>
839 <when value="flanking_floating_size">
840 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
841 </when>
842 </conditional>
843 </when>
844 <when value="bed">
845 <param type="select" name="further_information" label="Further information: Not required for bed input">
846 <option value="na">Not Required</option>
847 </param>
848 <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.">
849 <option value="automatic">Default</option>
850 <option value="0">Small</option>
851 <option value="1">Large</option>
852 </param>
853 <conditional name="flanking_region_option_source_type">
854 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
855 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
856 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
857 </param>
858 <when value="flanking_region_size">
859 <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"/>
860 </when>
861 <when value="flanking_floating_size">
862 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
863 </when>
864 </conditional>
865 </when>
866 </conditional>
867
868
869 <conditional name="numsamples">
870 <param type="select" name="numsamples2" label="Number of samples to plot">
871 <option value="1">1</option>
872 <option value="2">2</option>
873 <option value="3">3</option>
874 <option value="4">4</option>
875 <option value="5">5</option>
876 <option value="6">6</option>
877 <option value="7">7</option>
878 <option value="8">8</option>
879 <option value="9">9</option>
880 <option value="10">10</option>
881 </param>
882
883 <when value="1">
884 <conditional name="usepair">
885 <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.">
886 <option value="no">No</option>
887 <option value="yes">Yes</option>
888 </param>
889 <when value="no">
890 <!-- START: 1 sample, no refpairs, entry 1-->
891 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
892 <param type="hidden" name="reffile1" value="na"/>
893 <conditional name="genelist1">
894 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
895 <option value="no">Plot whole genome</option>
896 <option value="yes">Provide restricted gene list</option>
897 </param>
898 <when value="no">
899 <param type="hidden" name="genelist1" value="-1"/>
900 </when>
901 <when value="yes">
902 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
903 </when>
904 </conditional>
905 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
906 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
907 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
908 <!-- END: 1 sample, no refpairs, entry 1-->
909 </when>
910 <when value="yes">
911 <!-- START: 1 sample, yes refpairs, entry 1-->
912 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
913 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
914 <conditional name="genelist1">
915 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
916 <option value="no">Plot whole genome</option>
917 <option value="yes">Provide restricted gene list</option>
918 </param>
919 <when value="no">
920 <param type="hidden" name="genelist1" value="-1"/>
921 </when>
922 <when value="yes">
923 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
924 </when>
925 </conditional>
926 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
927 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
928 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
929 <!-- END: 1 sample, yes refpairs, entry 1-->
930 </when>
931 </conditional>
932 </when>
933 <when value="2">
934 <conditional name="usepair">
935 <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.">
936 <option value="no">No</option>
937 <option value="yes">Yes</option>
938 </param>
939 <when value="no">
940 <!-- START: 2 samples, no refpairs, entry 1-->
941 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
942 <param type="hidden" name="reffile1" value="na"/>
943 <conditional name="genelist1">
944 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
945 <option value="no">Plot whole genome</option>
946 <option value="yes">Provide restricted gene list</option>
947 </param>
948 <when value="no">
949 <param type="hidden" name="genelist1" value="-1"/>
950 </when>
951 <when value="yes">
952 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
953 </when>
954 </conditional>
955 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
956 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
957 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
958 <!-- END: 2 samples, no refpairs, entry 1-->
959 <!-- START: 2 samples, no refpairs, entry 2-->
960 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
961 <param type="hidden" name="reffile2" value="na"/>
962 <conditional name="genelist2">
963 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
964 <option value="no">Plot whole genome</option>
965 <option value="yes">Provide restricted gene list</option>
966 </param>
967 <when value="no">
968 <param type="hidden" name="genelist2" value="-1"/>
969 </when>
970 <when value="yes">
971 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
972 </when>
973 </conditional>
974 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
975 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
976 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
977 <!-- END: 2 samples, no refpairs, entry 2-->
978 </when>
979 <when value="yes">
980 <!-- START: 2 samples, yes refpairs, entry 1-->
981 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
982 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
983 <conditional name="genelist1">
984 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
985 <option value="no">Plot whole genome</option>
986 <option value="yes">Provide restricted gene list</option>
987 </param>
988 <when value="no">
989 <param type="hidden" name="genelist1" value="-1"/>
990 </when>
991 <when value="yes">
992 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
993 </when>
994 </conditional>
995 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
996 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
997 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
998 <!-- END: 2 samples, yes refpairs, entry 1-->
999 <!-- START: 2 samples, yes refpairs, entry 2-->
1000 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1001 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1002 <conditional name="genelist2">
1003 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1004 <option value="no">Plot whole genome</option>
1005 <option value="yes">Provide restricted gene list</option>
1006 </param>
1007 <when value="no">
1008 <param type="hidden" name="genelist2" value="-1"/>
1009 </when>
1010 <when value="yes">
1011 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1012 </when>
1013 </conditional>
1014 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1015 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1016 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1017 <!-- END: 2 samples, yes refpairs, entry 2-->
1018 </when>
1019 </conditional>
1020 </when>
1021 <when value="3">
1022 <conditional name="usepair">
1023 <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.">
1024 <option value="no">No</option>
1025 <option value="yes">Yes</option>
1026 </param>
1027 <when value="no">
1028 <!-- START: 3 samples, no refpairs, entry 1-->
1029 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1030 <param type="hidden" name="reffile1" value="na"/>
1031 <conditional name="genelist1">
1032 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1033 <option value="no">Plot whole genome</option>
1034 <option value="yes">Provide restricted gene list</option>
1035 </param>
1036 <when value="no">
1037 <param type="hidden" name="genelist1" value="-1"/>
1038 </when>
1039 <when value="yes">
1040 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1041 </when>
1042 </conditional>
1043 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1044 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1045 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1046 <!-- END: 3 samples, no refpairs, entry 1-->
1047 <!-- START: 3 samples, no refpairs, entry 2-->
1048 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1049 <param type="hidden" name="reffile2" value="na"/>
1050 <conditional name="genelist2">
1051 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1052 <option value="no">Plot whole genome</option>
1053 <option value="yes">Provide restricted gene list</option>
1054 </param>
1055 <when value="no">
1056 <param type="hidden" name="genelist2" value="-1"/>
1057 </when>
1058 <when value="yes">
1059 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1060 </when>
1061 </conditional>
1062 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1063 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1064 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1065 <!-- END: 3 samples, no refpairs, entry 2-->
1066 <!-- START: 3 samples, no refpairs, entry 3-->
1067 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1068 <param type="hidden" name="reffile3" value="na"/>
1069 <conditional name="genelist3">
1070 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1071 <option value="no">Plot whole genome</option>
1072 <option value="yes">Provide restricted gene list</option>
1073 </param>
1074 <when value="no">
1075 <param type="hidden" name="genelist3" value="-1"/>
1076 </when>
1077 <when value="yes">
1078 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1079 </when>
1080 </conditional>
1081 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1082 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1083 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1084 <!-- END: 3 samples, no refpairs, entry 3-->
1085 </when>
1086 <when value="yes">
1087 <!-- START: 3 samples, yes refpairs, entry 1-->
1088 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1089 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1090 <conditional name="genelist1">
1091 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1092 <option value="no">Plot whole genome</option>
1093 <option value="yes">Provide restricted gene list</option>
1094 </param>
1095 <when value="no">
1096 <param type="hidden" name="genelist1" value="-1"/>
1097 </when>
1098 <when value="yes">
1099 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1100 </when>
1101 </conditional>
1102 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1103 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1104 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1105 <!-- END: 3 samples, yes refpairs, entry 1-->
1106 <!-- START: 3 samples, yes refpairs, entry 2-->
1107 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1108 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1109 <conditional name="genelist2">
1110 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1111 <option value="no">Plot whole genome</option>
1112 <option value="yes">Provide restricted gene list</option>
1113 </param>
1114 <when value="no">
1115 <param type="hidden" name="genelist2" value="-1"/>
1116 </when>
1117 <when value="yes">
1118 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1119 </when>
1120 </conditional>
1121 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1122 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1123 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1124 <!-- END: 3 samples, yes refpairs, entry 2-->
1125 <!-- START: 3 samples, yes refpairs, entry 3-->
1126 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1127 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1128 <conditional name="genelist3">
1129 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1130 <option value="no">Plot whole genome</option>
1131 <option value="yes">Provide restricted gene list</option>
1132 </param>
1133 <when value="no">
1134 <param type="hidden" name="genelist3" value="-1"/>
1135 </when>
1136 <when value="yes">
1137 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1138 </when>
1139 </conditional>
1140 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1141 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1142 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1143 <!-- END: 3 samples, yes refpairs, entry 2-->
1144 </when>
1145 </conditional>
1146 </when>
1147 <when value="4">
1148 <conditional name="usepair">
1149 <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.">
1150 <option value="no">No</option>
1151 <option value="yes">Yes</option>
1152 </param>
1153 <when value="no">
1154 <!-- START: 4 samples, no refpairs, entry 1-->
1155 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1156 <param type="hidden" name="reffile1" value="na"/>
1157 <conditional name="genelist1">
1158 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1159 <option value="no">Plot whole genome</option>
1160 <option value="yes">Provide restricted gene list</option>
1161 </param>
1162 <when value="no">
1163 <param type="hidden" name="genelist1" value="-1"/>
1164 </when>
1165 <when value="yes">
1166 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1167 </when>
1168 </conditional>
1169 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1170 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1171 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1172 <!-- END: 4 samples, no refpairs, entry 1-->
1173 <!-- START: 4 samples, no refpairs, entry 2-->
1174 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1175 <param type="hidden" name="reffile2" value="na"/>
1176 <conditional name="genelist2">
1177 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1178 <option value="no">Plot whole genome</option>
1179 <option value="yes">Provide restricted gene list</option>
1180 </param>
1181 <when value="no">
1182 <param type="hidden" name="genelist2" value="-1"/>
1183 </when>
1184 <when value="yes">
1185 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1186 </when>
1187 </conditional>
1188 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1189 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1190 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1191 <!-- END: 4 samples, no refpairs, entry 2-->
1192 <!-- START: 4 samples, no refpairs, entry 3-->
1193 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1194 <param type="hidden" name="reffile3" value="na"/>
1195 <conditional name="genelist3">
1196 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1197 <option value="no">Plot whole genome</option>
1198 <option value="yes">Provide restricted gene list</option>
1199 </param>
1200 <when value="no">
1201 <param type="hidden" name="genelist3" value="-1"/>
1202 </when>
1203 <when value="yes">
1204 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1205 </when>
1206 </conditional>
1207 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1208 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1209 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1210 <!-- END: 4 samples, no refpairs, entry 3-->
1211 <!-- START: 4 samples, no refpairs, entry 4-->
1212 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1213 <param type="hidden" name="reffile4" value="na"/>
1214 <conditional name="genelist4">
1215 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1216 <option value="no">Plot whole genome</option>
1217 <option value="yes">Provide restricted gene list</option>
1218 </param>
1219 <when value="no">
1220 <param type="hidden" name="genelist4" value="-1"/>
1221 </when>
1222 <when value="yes">
1223 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1224 </when>
1225 </conditional>
1226 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1227 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1228 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1229 <!-- END: 4 samples, no refpairs, entry 4-->
1230 </when>
1231 <when value="yes">
1232 <!-- START: 4 samples, yes refpairs, entry 1-->
1233 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1234 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1235 <conditional name="genelist1">
1236 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1237 <option value="no">Plot whole genome</option>
1238 <option value="yes">Provide restricted gene list</option>
1239 </param>
1240 <when value="no">
1241 <param type="hidden" name="genelist1" value="-1"/>
1242 </when>
1243 <when value="yes">
1244 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1245 </when>
1246 </conditional>
1247 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1248 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1249 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1250 <!-- END: 4 samples, yes refpairs, entry 1-->
1251 <!-- START: 4 samples, yes refpairs, entry 2-->
1252 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1253 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1254 <conditional name="genelist2">
1255 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1256 <option value="no">Plot whole genome</option>
1257 <option value="yes">Provide restricted gene list</option>
1258 </param>
1259 <when value="no">
1260 <param type="hidden" name="genelist2" value="-1"/>
1261 </when>
1262 <when value="yes">
1263 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1264 </when>
1265 </conditional>
1266 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1267 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1268 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1269 <!-- END: 4 samples, yes refpairs, entry 2-->
1270 <!-- START: 4 samples, yes refpairs, entry 3-->
1271 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1272 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1273 <conditional name="genelist3">
1274 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1275 <option value="no">Plot whole genome</option>
1276 <option value="yes">Provide restricted gene list</option>
1277 </param>
1278 <when value="no">
1279 <param type="hidden" name="genelist3" value="-1"/>
1280 </when>
1281 <when value="yes">
1282 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1283 </when>
1284 </conditional>
1285 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1286 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1287 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1288 <!-- END: 4 samples, yes refpairs, entry 3-->
1289 <!-- START: 4 samples, yes refpairs, entry 4-->
1290 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1291 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
1292 <conditional name="genelist4">
1293 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1294 <option value="no">Plot whole genome</option>
1295 <option value="yes">Provide restricted gene list</option>
1296 </param>
1297 <when value="no">
1298 <param type="hidden" name="genelist4" value="-1"/>
1299 </when>
1300 <when value="yes">
1301 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1302 </when>
1303 </conditional>
1304 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1305 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1306 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1307 <!-- END: 4 samples, yes refpairs, entry 4-->
1308 </when>
1309 </conditional>
1310 </when>
1311 <when value="5">
1312 <conditional name="usepair">
1313 <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.">
1314 <option value="no">No</option>
1315 <option value="yes">Yes</option>
1316 </param>
1317 <when value="no">
1318 <!-- START: 5 samples, no refpairs, entry 1-->
1319 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1320 <param type="hidden" name="reffile1" value="na"/>
1321 <conditional name="genelist1">
1322 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1323 <option value="no">Plot whole genome</option>
1324 <option value="yes">Provide restricted gene list</option>
1325 </param>
1326 <when value="no">
1327 <param type="hidden" name="genelist1" value="-1"/>
1328 </when>
1329 <when value="yes">
1330 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1331 </when>
1332 </conditional>
1333 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1334 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1335 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1336 <!-- END: 5 samples, no refpairs, entry 1-->
1337 <!-- START: 5 samples, no refpairs, entry 2-->
1338 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1339 <param type="hidden" name="reffile2" value="na"/>
1340 <conditional name="genelist2">
1341 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1342 <option value="no">Plot whole genome</option>
1343 <option value="yes">Provide restricted gene list</option>
1344 </param>
1345 <when value="no">
1346 <param type="hidden" name="genelist2" value="-1"/>
1347 </when>
1348 <when value="yes">
1349 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1350 </when>
1351 </conditional>
1352 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1353 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1354 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1355 <!-- END: 5 samples, no refpairs, entry 2-->
1356 <!-- START: 5 samples, no refpairs, entry 3-->
1357 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1358 <param type="hidden" name="reffile3" value="na"/>
1359 <conditional name="genelist3">
1360 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1361 <option value="no">Plot whole genome</option>
1362 <option value="yes">Provide restricted gene list</option>
1363 </param>
1364 <when value="no">
1365 <param type="hidden" name="genelist3" value="-1"/>
1366 </when>
1367 <when value="yes">
1368 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1369 </when>
1370 </conditional>
1371 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1372 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1373 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1374 <!-- END: 5 samples, no refpairs, entry 3-->
1375 <!-- START: 5 samples, no refpairs, entry 4-->
1376 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1377 <param type="hidden" name="reffile4" value="na"/>
1378 <conditional name="genelist4">
1379 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1380 <option value="no">Plot whole genome</option>
1381 <option value="yes">Provide restricted gene list</option>
1382 </param>
1383 <when value="no">
1384 <param type="hidden" name="genelist4" value="-1"/>
1385 </when>
1386 <when value="yes">
1387 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1388 </when>
1389 </conditional>
1390 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1391 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1392 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1393 <!-- END: 5 samples, no refpairs, entry 4-->
1394 <!-- START: 5 samples, no refpairs, entry 5-->
1395 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1396 <param type="hidden" name="reffile5" value="na"/>
1397 <conditional name="genelist5">
1398 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1399 <option value="no">Plot whole genome</option>
1400 <option value="yes">Provide restricted gene list</option>
1401 </param>
1402 <when value="no">
1403 <param type="hidden" name="genelist5" value="-1"/>
1404 </when>
1405 <when value="yes">
1406 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1407 </when>
1408 </conditional>
1409 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1410 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1411 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1412 <!-- END: 5 samples, no refpairs, entry 5-->
1413 </when>
1414 <when value="yes">
1415 <!-- START: 5 samples, yes refpairs, entry 1-->
1416 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1417 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1418 <conditional name="genelist1">
1419 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1420 <option value="no">Plot whole genome</option>
1421 <option value="yes">Provide restricted gene list</option>
1422 </param>
1423 <when value="no">
1424 <param type="hidden" name="genelist1" value="-1"/>
1425 </when>
1426 <when value="yes">
1427 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1428 </when>
1429 </conditional>
1430 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1431 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1432 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1433 <!-- END: 5 samples, yes refpairs, entry 1-->
1434 <!-- START: 5 samples, yes refpairs, entry 2-->
1435 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1436 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1437 <conditional name="genelist2">
1438 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1439 <option value="no">Plot whole genome</option>
1440 <option value="yes">Provide restricted gene list</option>
1441 </param>
1442 <when value="no">
1443 <param type="hidden" name="genelist2" value="-1"/>
1444 </when>
1445 <when value="yes">
1446 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1447 </when>
1448 </conditional>
1449 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1450 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1451 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1452 <!-- END: 5 samples, yes refpairs, entry 2-->
1453 <!-- START: 5 samples, yes refpairs, entry 3-->
1454 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1455 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1456 <conditional name="genelist3">
1457 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1458 <option value="no">Plot whole genome</option>
1459 <option value="yes">Provide restricted gene list</option>
1460 </param>
1461 <when value="no">
1462 <param type="hidden" name="genelist3" value="-1"/>
1463 </when>
1464 <when value="yes">
1465 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1466 </when>
1467 </conditional>
1468 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1469 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1470 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1471 <!-- END: 5 samples, yes refpairs, entry 3-->
1472 <!-- START: 5 samples, yes refpairs, entry 4-->
1473 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1474 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
1475 <conditional name="genelist4">
1476 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1477 <option value="no">Plot whole genome</option>
1478 <option value="yes">Provide restricted gene list</option>
1479 </param>
1480 <when value="no">
1481 <param type="hidden" name="genelist4" value="-1"/>
1482 </when>
1483 <when value="yes">
1484 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1485 </when>
1486 </conditional>
1487 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1488 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1489 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1490 <!-- END: 5 samples, yes refpairs, entry 4-->
1491 <!-- START: 5 samples, yes refpairs, entry 5-->
1492 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1493 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
1494 <conditional name="genelist5">
1495 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1496 <option value="no">Plot whole genome</option>
1497 <option value="yes">Provide restricted gene list</option>
1498 </param>
1499 <when value="no">
1500 <param type="hidden" name="genelist5" value="-1"/>
1501 </when>
1502 <when value="yes">
1503 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1504 </when>
1505 </conditional>
1506 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1507 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1508 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1509 <!-- END: 5 samples, yes refpairs, entry 5-->
1510 </when>
1511 </conditional>
1512 </when>
1513 <when value="6">
1514 <conditional name="usepair">
1515 <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.">
1516 <option value="no">No</option>
1517 <option value="yes">Yes</option>
1518 </param>
1519 <when value="no">
1520 <!-- START: 6 samples, no refpairs, entry 1-->
1521 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1522 <param type="hidden" name="reffile1" value="na"/>
1523 <conditional name="genelist1">
1524 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1525 <option value="no">Plot whole genome</option>
1526 <option value="yes">Provide restricted gene list</option>
1527 </param>
1528 <when value="no">
1529 <param type="hidden" name="genelist1" value="-1"/>
1530 </when>
1531 <when value="yes">
1532 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1533 </when>
1534 </conditional>
1535 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1536 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1537 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1538 <!-- END: 6 samples, no refpairs, entry 1-->
1539 <!-- START: 6 samples, no refpairs, entry 2-->
1540 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1541 <param type="hidden" name="reffile2" value="na"/>
1542 <conditional name="genelist2">
1543 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1544 <option value="no">Plot whole genome</option>
1545 <option value="yes">Provide restricted gene list</option>
1546 </param>
1547 <when value="no">
1548 <param type="hidden" name="genelist2" value="-1"/>
1549 </when>
1550 <when value="yes">
1551 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1552 </when>
1553 </conditional>
1554 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1555 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1556 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1557 <!-- END: 6 samples, no refpairs, entry 2-->
1558 <!-- START: 6 samples, no refpairs, entry 3-->
1559 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1560 <param type="hidden" name="reffile3" value="na"/>
1561 <conditional name="genelist3">
1562 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1563 <option value="no">Plot whole genome</option>
1564 <option value="yes">Provide restricted gene list</option>
1565 </param>
1566 <when value="no">
1567 <param type="hidden" name="genelist3" value="-1"/>
1568 </when>
1569 <when value="yes">
1570 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1571 </when>
1572 </conditional>
1573 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1574 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1575 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1576 <!-- END: 6 samples, no refpairs, entry 3-->
1577 <!-- START: 6 samples, no refpairs, entry 4-->
1578 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1579 <param type="hidden" name="reffile4" value="na"/>
1580 <conditional name="genelist4">
1581 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1582 <option value="no">Plot whole genome</option>
1583 <option value="yes">Provide restricted gene list</option>
1584 </param>
1585 <when value="no">
1586 <param type="hidden" name="genelist4" value="-1"/>
1587 </when>
1588 <when value="yes">
1589 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1590 </when>
1591 </conditional>
1592 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1593 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1594 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1595 <!-- END: 6 samples, no refpairs, entry 4-->
1596 <!-- START: 6 samples, no refpairs, entry 5-->
1597 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1598 <param type="hidden" name="reffile5" value="na"/>
1599 <conditional name="genelist5">
1600 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1601 <option value="no">Plot whole genome</option>
1602 <option value="yes">Provide restricted gene list</option>
1603 </param>
1604 <when value="no">
1605 <param type="hidden" name="genelist5" value="-1"/>
1606 </when>
1607 <when value="yes">
1608 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1609 </when>
1610 </conditional>
1611 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1612 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1613 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1614 <!-- END: 6 samples, no refpairs, entry 5-->
1615 <!-- START: 6 samples, no refpairs, entry 6-->
1616 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
1617 <param type="hidden" name="reffile6" value="na"/>
1618 <conditional name="genelist6">
1619 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
1620 <option value="no">Plot whole genome</option>
1621 <option value="yes">Provide restricted gene list</option>
1622 </param>
1623 <when value="no">
1624 <param type="hidden" name="genelist6" value="-1"/>
1625 </when>
1626 <when value="yes">
1627 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
1628 </when>
1629 </conditional>
1630 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
1631 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
1632 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
1633 <!-- END: 6 samples, no refpairs, entry 6-->
1634 </when>
1635 <when value="yes">
1636 <!-- START: 6 samples, yes refpairs, entry 1-->
1637 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1638 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1639 <conditional name="genelist1">
1640 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1641 <option value="no">Plot whole genome</option>
1642 <option value="yes">Provide restricted gene list</option>
1643 </param>
1644 <when value="no">
1645 <param type="hidden" name="genelist1" value="-1"/>
1646 </when>
1647 <when value="yes">
1648 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1649 </when>
1650 </conditional>
1651 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1652 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1653 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1654 <!-- END: 6 samples, yes refpairs, entry 1-->
1655 <!-- START: 6 samples, yes refpairs, entry 2-->
1656 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1657 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1658 <conditional name="genelist2">
1659 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1660 <option value="no">Plot whole genome</option>
1661 <option value="yes">Provide restricted gene list</option>
1662 </param>
1663 <when value="no">
1664 <param type="hidden" name="genelist2" value="-1"/>
1665 </when>
1666 <when value="yes">
1667 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1668 </when>
1669 </conditional>
1670 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1671 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1672 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1673 <!-- END: 6 samples, yes refpairs, entry 2-->
1674 <!-- START: 6 samples, yes refpairs, entry 3-->
1675 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1676 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1677 <conditional name="genelist3">
1678 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1679 <option value="no">Plot whole genome</option>
1680 <option value="yes">Provide restricted gene list</option>
1681 </param>
1682 <when value="no">
1683 <param type="hidden" name="genelist3" value="-1"/>
1684 </when>
1685 <when value="yes">
1686 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1687 </when>
1688 </conditional>
1689 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1690 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1691 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1692 <!-- END: 6 samples, yes refpairs, entry 3-->
1693 <!-- START: 6 samples, yes refpairs, entry 4-->
1694 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1695 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
1696 <conditional name="genelist4">
1697 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1698 <option value="no">Plot whole genome</option>
1699 <option value="yes">Provide restricted gene list</option>
1700 </param>
1701 <when value="no">
1702 <param type="hidden" name="genelist4" value="-1"/>
1703 </when>
1704 <when value="yes">
1705 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1706 </when>
1707 </conditional>
1708 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1709 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1710 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1711 <!-- END: 6 samples, yes refpairs, entry 4-->
1712 <!-- START: 6 samples, yes refpairs, entry 5-->
1713 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1714 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
1715 <conditional name="genelist5">
1716 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1717 <option value="no">Plot whole genome</option>
1718 <option value="yes">Provide restricted gene list</option>
1719 </param>
1720 <when value="no">
1721 <param type="hidden" name="genelist5" value="-1"/>
1722 </when>
1723 <when value="yes">
1724 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1725 </when>
1726 </conditional>
1727 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1728 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1729 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1730 <!-- END: 6 samples, yes refpairs, entry 5-->
1731 <!-- START: 6 samples, yes refpairs, entry 6-->
1732 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
1733 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
1734 <conditional name="genelist6">
1735 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
1736 <option value="no">Plot whole genome</option>
1737 <option value="yes">Provide restricted gene list</option>
1738 </param>
1739 <when value="no">
1740 <param type="hidden" name="genelist6" value="-1"/>
1741 </when>
1742 <when value="yes">
1743 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
1744 </when>
1745 </conditional>
1746 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
1747 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
1748 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
1749 <!-- END: 6 samples, yes refpairs, entry 6-->
1750 </when>
1751 </conditional>
1752 </when>
1753 <when value="7">
1754 <conditional name="usepair">
1755 <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.">
1756 <option value="no">No</option>
1757 <option value="yes">Yes</option>
1758 </param>
1759 <when value="no">
1760 <!-- START: 7 samples, no refpairs, entry 1-->
1761 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1762 <param type="hidden" name="reffile1" value="na"/>
1763 <conditional name="genelist1">
1764 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1765 <option value="no">Plot whole genome</option>
1766 <option value="yes">Provide restricted gene list</option>
1767 </param>
1768 <when value="no">
1769 <param type="hidden" name="genelist1" value="-1"/>
1770 </when>
1771 <when value="yes">
1772 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1773 </when>
1774 </conditional>
1775 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1776 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1777 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1778 <!-- END: 7 samples, no refpairs, entry 1-->
1779 <!-- START: 7 samples, no refpairs, entry 2-->
1780 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1781 <param type="hidden" name="reffile2" value="na"/>
1782 <conditional name="genelist2">
1783 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1784 <option value="no">Plot whole genome</option>
1785 <option value="yes">Provide restricted gene list</option>
1786 </param>
1787 <when value="no">
1788 <param type="hidden" name="genelist2" value="-1"/>
1789 </when>
1790 <when value="yes">
1791 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1792 </when>
1793 </conditional>
1794 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1795 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1796 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1797 <!-- END: 7 samples, no refpairs, entry 2-->
1798 <!-- START: 7 samples, no refpairs, entry 3-->
1799 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1800 <param type="hidden" name="reffile3" value="na"/>
1801 <conditional name="genelist3">
1802 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1803 <option value="no">Plot whole genome</option>
1804 <option value="yes">Provide restricted gene list</option>
1805 </param>
1806 <when value="no">
1807 <param type="hidden" name="genelist3" value="-1"/>
1808 </when>
1809 <when value="yes">
1810 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1811 </when>
1812 </conditional>
1813 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1814 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1815 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1816 <!-- END: 7 samples, no refpairs, entry 3-->
1817 <!-- START: 7 samples, no refpairs, entry 4-->
1818 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1819 <param type="hidden" name="reffile4" value="na"/>
1820 <conditional name="genelist4">
1821 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1822 <option value="no">Plot whole genome</option>
1823 <option value="yes">Provide restricted gene list</option>
1824 </param>
1825 <when value="no">
1826 <param type="hidden" name="genelist4" value="-1"/>
1827 </when>
1828 <when value="yes">
1829 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1830 </when>
1831 </conditional>
1832 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1833 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1834 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1835 <!-- END: 7 samples, no refpairs, entry 4-->
1836 <!-- START: 7 samples, no refpairs, entry 5-->
1837 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1838 <param type="hidden" name="reffile5" value="na"/>
1839 <conditional name="genelist5">
1840 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1841 <option value="no">Plot whole genome</option>
1842 <option value="yes">Provide restricted gene list</option>
1843 </param>
1844 <when value="no">
1845 <param type="hidden" name="genelist5" value="-1"/>
1846 </when>
1847 <when value="yes">
1848 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1849 </when>
1850 </conditional>
1851 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1852 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1853 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1854 <!-- END: 7 samples, no refpairs, entry 5-->
1855 <!-- START: 7 samples, no refpairs, entry 6-->
1856 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
1857 <param type="hidden" name="reffile6" value="na"/>
1858 <conditional name="genelist6">
1859 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
1860 <option value="no">Plot whole genome</option>
1861 <option value="yes">Provide restricted gene list</option>
1862 </param>
1863 <when value="no">
1864 <param type="hidden" name="genelist6" value="-1"/>
1865 </when>
1866 <when value="yes">
1867 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
1868 </when>
1869 </conditional>
1870 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
1871 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
1872 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
1873 <!-- END: 7 samples, no refpairs, entry 6-->
1874 <!-- START: 7 samples, no refpairs, entry 7-->
1875 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
1876 <param type="hidden" name="reffile7" value="na"/>
1877 <conditional name="genelist7">
1878 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
1879 <option value="no">Plot whole genome</option>
1880 <option value="yes">Provide restricted gene list</option>
1881 </param>
1882 <when value="no">
1883 <param type="hidden" name="genelist7" value="-1"/>
1884 </when>
1885 <when value="yes">
1886 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
1887 </when>
1888 </conditional>
1889 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
1890 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
1891 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
1892 <!-- END: 7 samples, no refpairs, entry 7-->
1893 </when>
1894 <when value="yes">
1895 <!-- START: 7 samples, yes refpairs, entry 1-->
1896 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
1897 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
1898 <conditional name="genelist1">
1899 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
1900 <option value="no">Plot whole genome</option>
1901 <option value="yes">Provide restricted gene list</option>
1902 </param>
1903 <when value="no">
1904 <param type="hidden" name="genelist1" value="-1"/>
1905 </when>
1906 <when value="yes">
1907 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
1908 </when>
1909 </conditional>
1910 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
1911 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
1912 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
1913 <!-- END: 7 samples, yes refpairs, entry 1-->
1914 <!-- START: 7 samples, yes refpairs, entry 2-->
1915 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
1916 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
1917 <conditional name="genelist2">
1918 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
1919 <option value="no">Plot whole genome</option>
1920 <option value="yes">Provide restricted gene list</option>
1921 </param>
1922 <when value="no">
1923 <param type="hidden" name="genelist2" value="-1"/>
1924 </when>
1925 <when value="yes">
1926 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
1927 </when>
1928 </conditional>
1929 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
1930 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
1931 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
1932 <!-- END: 7 samples, yes refpairs, entry 2-->
1933 <!-- START: 7 samples, yes refpairs, entry 3-->
1934 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
1935 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
1936 <conditional name="genelist3">
1937 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
1938 <option value="no">Plot whole genome</option>
1939 <option value="yes">Provide restricted gene list</option>
1940 </param>
1941 <when value="no">
1942 <param type="hidden" name="genelist3" value="-1"/>
1943 </when>
1944 <when value="yes">
1945 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
1946 </when>
1947 </conditional>
1948 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
1949 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
1950 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
1951 <!-- END: 7 samples, yes refpairs, entry 3-->
1952 <!-- START: 7 samples, yes refpairs, entry 4-->
1953 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
1954 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
1955 <conditional name="genelist4">
1956 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
1957 <option value="no">Plot whole genome</option>
1958 <option value="yes">Provide restricted gene list</option>
1959 </param>
1960 <when value="no">
1961 <param type="hidden" name="genelist4" value="-1"/>
1962 </when>
1963 <when value="yes">
1964 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
1965 </when>
1966 </conditional>
1967 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
1968 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
1969 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
1970 <!-- END: 7 samples, yes refpairs, entry 4-->
1971 <!-- START: 7 samples, yes refpairs, entry 5-->
1972 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
1973 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
1974 <conditional name="genelist5">
1975 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
1976 <option value="no">Plot whole genome</option>
1977 <option value="yes">Provide restricted gene list</option>
1978 </param>
1979 <when value="no">
1980 <param type="hidden" name="genelist5" value="-1"/>
1981 </when>
1982 <when value="yes">
1983 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
1984 </when>
1985 </conditional>
1986 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
1987 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
1988 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
1989 <!-- END: 7 samples, yes refpairs, entry 5-->
1990 <!-- START: 7 samples, yes refpairs, entry 6-->
1991 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
1992 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
1993 <conditional name="genelist6">
1994 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
1995 <option value="no">Plot whole genome</option>
1996 <option value="yes">Provide restricted gene list</option>
1997 </param>
1998 <when value="no">
1999 <param type="hidden" name="genelist6" value="-1"/>
2000 </when>
2001 <when value="yes">
2002 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2003 </when>
2004 </conditional>
2005 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2006 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2007 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2008 <!-- END: 7 samples, yes refpairs, entry 6-->
2009 <!-- START: 7 samples, yes refpairs, entry 7-->
2010 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2011 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
2012 <conditional name="genelist7">
2013 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2014 <option value="no">Plot whole genome</option>
2015 <option value="yes">Provide restricted gene list</option>
2016 </param>
2017 <when value="no">
2018 <param type="hidden" name="genelist7" value="-1"/>
2019 </when>
2020 <when value="yes">
2021 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2022 </when>
2023 </conditional>
2024 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2025 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2026 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2027 <!-- END: 7 samples, yes refpairs, entry 7-->
2028 </when>
2029 </conditional>
2030 </when>
2031 <when value="8">
2032 <conditional name="usepair">
2033 <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.">
2034 <option value="no">No</option>
2035 <option value="yes">Yes</option>
2036 </param>
2037 <when value="no">
2038 <!-- START: 8 samples, no refpairs, entry 1-->
2039 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2040 <param type="hidden" name="reffile1" value="na"/>
2041 <conditional name="genelist1">
2042 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2043 <option value="no">Plot whole genome</option>
2044 <option value="yes">Provide restricted gene list</option>
2045 </param>
2046 <when value="no">
2047 <param type="hidden" name="genelist1" value="-1"/>
2048 </when>
2049 <when value="yes">
2050 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2051 </when>
2052 </conditional>
2053 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2054 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2055 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2056 <!-- END: 8 samples, no refpairs, entry 1-->
2057 <!-- START: 8 samples, no refpairs, entry 2-->
2058 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2059 <param type="hidden" name="reffile2" value="na"/>
2060 <conditional name="genelist2">
2061 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2062 <option value="no">Plot whole genome</option>
2063 <option value="yes">Provide restricted gene list</option>
2064 </param>
2065 <when value="no">
2066 <param type="hidden" name="genelist2" value="-1"/>
2067 </when>
2068 <when value="yes">
2069 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2070 </when>
2071 </conditional>
2072 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2073 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2074 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2075 <!-- END: 8 samples, no refpairs, entry 2-->
2076 <!-- START: 8 samples, no refpairs, entry 3-->
2077 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2078 <param type="hidden" name="reffile3" value="na"/>
2079 <conditional name="genelist3">
2080 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2081 <option value="no">Plot whole genome</option>
2082 <option value="yes">Provide restricted gene list</option>
2083 </param>
2084 <when value="no">
2085 <param type="hidden" name="genelist3" value="-1"/>
2086 </when>
2087 <when value="yes">
2088 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2089 </when>
2090 </conditional>
2091 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2092 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2093 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2094 <!-- END: 8 samples, no refpairs, entry 3-->
2095 <!-- START: 8 samples, no refpairs, entry 4-->
2096 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2097 <param type="hidden" name="reffile4" value="na"/>
2098 <conditional name="genelist4">
2099 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2100 <option value="no">Plot whole genome</option>
2101 <option value="yes">Provide restricted gene list</option>
2102 </param>
2103 <when value="no">
2104 <param type="hidden" name="genelist4" value="-1"/>
2105 </when>
2106 <when value="yes">
2107 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2108 </when>
2109 </conditional>
2110 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2111 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2112 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2113 <!-- END: 8 samples, no refpairs, entry 4-->
2114 <!-- START: 8 samples, no refpairs, entry 5-->
2115 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2116 <param type="hidden" name="reffile5" value="na"/>
2117 <conditional name="genelist5">
2118 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2119 <option value="no">Plot whole genome</option>
2120 <option value="yes">Provide restricted gene list</option>
2121 </param>
2122 <when value="no">
2123 <param type="hidden" name="genelist5" value="-1"/>
2124 </when>
2125 <when value="yes">
2126 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2127 </when>
2128 </conditional>
2129 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2130 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2131 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2132 <!-- END: 8 samples, no refpairs, entry 5-->
2133 <!-- START: 8 samples, no refpairs, entry 6-->
2134 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2135 <param type="hidden" name="reffile6" value="na"/>
2136 <conditional name="genelist6">
2137 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2138 <option value="no">Plot whole genome</option>
2139 <option value="yes">Provide restricted gene list</option>
2140 </param>
2141 <when value="no">
2142 <param type="hidden" name="genelist6" value="-1"/>
2143 </when>
2144 <when value="yes">
2145 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2146 </when>
2147 </conditional>
2148 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2149 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2150 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2151 <!-- END: 8 samples, no refpairs, entry 6-->
2152 <!-- START: 8 samples, no refpairs, entry 7-->
2153 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2154 <param type="hidden" name="reffile7" value="na"/>
2155 <conditional name="genelist7">
2156 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2157 <option value="no">Plot whole genome</option>
2158 <option value="yes">Provide restricted gene list</option>
2159 </param>
2160 <when value="no">
2161 <param type="hidden" name="genelist7" value="-1"/>
2162 </when>
2163 <when value="yes">
2164 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2165 </when>
2166 </conditional>
2167 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2168 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2169 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2170 <!-- END: 8 samples, no refpairs, entry 7-->
2171 <!-- START: 8 samples, no refpairs, entry 8-->
2172 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2173 <param type="hidden" name="reffile8" value="na"/>
2174 <conditional name="genelist7">
2175 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2176 <option value="no">Plot whole genome</option>
2177 <option value="yes">Provide restricted gene list</option>
2178 </param>
2179 <when value="no">
2180 <param type="hidden" name="genelist8" value="-1"/>
2181 </when>
2182 <when value="yes">
2183 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2184 </when>
2185 </conditional>
2186 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2187 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2188 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2189 <!-- END: 8 samples, no refpairs, entry 8-->
2190 </when>
2191 <when value="yes">
2192 <!-- START: 8 samples, yes refpairs, entry 1-->
2193 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2194 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
2195 <conditional name="genelist1">
2196 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2197 <option value="no">Plot whole genome</option>
2198 <option value="yes">Provide restricted gene list</option>
2199 </param>
2200 <when value="no">
2201 <param type="hidden" name="genelist1" value="-1"/>
2202 </when>
2203 <when value="yes">
2204 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2205 </when>
2206 </conditional>
2207 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2208 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2209 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2210 <!-- END: 8 samples, yes refpairs, entry 1-->
2211 <!-- START: 8 samples, yes refpairs, entry 2-->
2212 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2213 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
2214 <conditional name="genelist2">
2215 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2216 <option value="no">Plot whole genome</option>
2217 <option value="yes">Provide restricted gene list</option>
2218 </param>
2219 <when value="no">
2220 <param type="hidden" name="genelist2" value="-1"/>
2221 </when>
2222 <when value="yes">
2223 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2224 </when>
2225 </conditional>
2226 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2227 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2228 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2229 <!-- END: 8 samples, yes refpairs, entry 2-->
2230 <!-- START: 8 samples, yes refpairs, entry 3-->
2231 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2232 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
2233 <conditional name="genelist3">
2234 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2235 <option value="no">Plot whole genome</option>
2236 <option value="yes">Provide restricted gene list</option>
2237 </param>
2238 <when value="no">
2239 <param type="hidden" name="genelist3" value="-1"/>
2240 </when>
2241 <when value="yes">
2242 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2243 </when>
2244 </conditional>
2245 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2246 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2247 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2248 <!-- END: 8 samples, yes refpairs, entry 3-->
2249 <!-- START: 8 samples, yes refpairs, entry 4-->
2250 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2251 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
2252 <conditional name="genelist4">
2253 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2254 <option value="no">Plot whole genome</option>
2255 <option value="yes">Provide restricted gene list</option>
2256 </param>
2257 <when value="no">
2258 <param type="hidden" name="genelist4" value="-1"/>
2259 </when>
2260 <when value="yes">
2261 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2262 </when>
2263 </conditional>
2264 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2265 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2266 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2267 <!-- END: 8 samples, yes refpairs, entry 4-->
2268 <!-- START: 8 samples, yes refpairs, entry 5-->
2269 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2270 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
2271 <conditional name="genelist5">
2272 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2273 <option value="no">Plot whole genome</option>
2274 <option value="yes">Provide restricted gene list</option>
2275 </param>
2276 <when value="no">
2277 <param type="hidden" name="genelist5" value="-1"/>
2278 </when>
2279 <when value="yes">
2280 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2281 </when>
2282 </conditional>
2283 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2284 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2285 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2286 <!-- END: 8 samples, yes refpairs, entry 5-->
2287 <!-- START: 8 samples, yes refpairs, entry 6-->
2288 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2289 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
2290 <conditional name="genelist6">
2291 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2292 <option value="no">Plot whole genome</option>
2293 <option value="yes">Provide restricted gene list</option>
2294 </param>
2295 <when value="no">
2296 <param type="hidden" name="genelist6" value="-1"/>
2297 </when>
2298 <when value="yes">
2299 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2300 </when>
2301 </conditional>
2302 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2303 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2304 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2305 <!-- END: 8 samples, yes refpairs, entry 6-->
2306 <!-- START: 8 samples, yes refpairs, entry 7-->
2307 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2308 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
2309 <conditional name="genelist7">
2310 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2311 <option value="no">Plot whole genome</option>
2312 <option value="yes">Provide restricted gene list</option>
2313 </param>
2314 <when value="no">
2315 <param type="hidden" name="genelist7" value="-1"/>
2316 </when>
2317 <when value="yes">
2318 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2319 </when>
2320 </conditional>
2321 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2322 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2323 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2324 <!-- END: 8 samples, yes refpairs, entry 7-->
2325 <!-- START: 8 samples, yes refpairs, entry 8-->
2326 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2327 <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/>
2328 <conditional name="genelist8">
2329 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2330 <option value="no">Plot whole genome</option>
2331 <option value="yes">Provide restricted gene list</option>
2332 </param>
2333 <when value="no">
2334 <param type="hidden" name="genelist8" value="-1"/>
2335 </when>
2336 <when value="yes">
2337 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2338 </when>
2339 </conditional>
2340 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2341 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2342 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2343 <!-- END: 8 samples, yes refpairs, entry 8-->
2344 </when>
2345 </conditional>
2346 </when>
2347 <when value="9">
2348 <conditional name="usepair">
2349 <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.">
2350 <option value="no">No</option>
2351 <option value="yes">Yes</option>
2352 </param>
2353 <when value="no">
2354 <!-- START: 9 samples, no refpairs, entry 1-->
2355 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2356 <param type="hidden" name="reffile1" value="na"/>
2357 <conditional name="genelist1">
2358 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2359 <option value="no">Plot whole genome</option>
2360 <option value="yes">Provide restricted gene list</option>
2361 </param>
2362 <when value="no">
2363 <param type="hidden" name="genelist1" value="-1"/>
2364 </when>
2365 <when value="yes">
2366 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2367 </when>
2368 </conditional>
2369 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2370 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2371 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2372 <!-- END: 9 samples, no refpairs, entry 1-->
2373 <!-- START: 9 samples, no refpairs, entry 2-->
2374 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2375 <param type="hidden" name="reffile2" value="na"/>
2376 <conditional name="genelist2">
2377 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2378 <option value="no">Plot whole genome</option>
2379 <option value="yes">Provide restricted gene list</option>
2380 </param>
2381 <when value="no">
2382 <param type="hidden" name="genelist2" value="-1"/>
2383 </when>
2384 <when value="yes">
2385 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2386 </when>
2387 </conditional>
2388 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2389 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2390 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2391 <!-- END: 9 samples, no refpairs, entry 2-->
2392 <!-- START: 9 samples, no refpairs, entry 3-->
2393 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2394 <param type="hidden" name="reffile3" value="na"/>
2395 <conditional name="genelist3">
2396 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2397 <option value="no">Plot whole genome</option>
2398 <option value="yes">Provide restricted gene list</option>
2399 </param>
2400 <when value="no">
2401 <param type="hidden" name="genelist3" value="-1"/>
2402 </when>
2403 <when value="yes">
2404 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2405 </when>
2406 </conditional>
2407 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2408 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2409 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2410 <!-- END: 9 samples, no refpairs, entry 3-->
2411 <!-- START: 9 samples, no refpairs, entry 4-->
2412 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2413 <param type="hidden" name="reffile4" value="na"/>
2414 <conditional name="genelist4">
2415 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2416 <option value="no">Plot whole genome</option>
2417 <option value="yes">Provide restricted gene list</option>
2418 </param>
2419 <when value="no">
2420 <param type="hidden" name="genelist4" value="-1"/>
2421 </when>
2422 <when value="yes">
2423 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2424 </when>
2425 </conditional>
2426 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2427 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2428 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2429 <!-- END: 9 samples, no refpairs, entry 4-->
2430 <!-- START: 9 samples, no refpairs, entry 5-->
2431 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2432 <param type="hidden" name="reffile5" value="na"/>
2433 <conditional name="genelist5">
2434 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2435 <option value="no">Plot whole genome</option>
2436 <option value="yes">Provide restricted gene list</option>
2437 </param>
2438 <when value="no">
2439 <param type="hidden" name="genelist5" value="-1"/>
2440 </when>
2441 <when value="yes">
2442 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2443 </when>
2444 </conditional>
2445 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2446 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2447 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2448 <!-- END: 9 samples, no refpairs, entry 5-->
2449 <!-- START: 9 samples, no refpairs, entry 6-->
2450 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2451 <param type="hidden" name="reffile6" value="na"/>
2452 <conditional name="genelist6">
2453 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2454 <option value="no">Plot whole genome</option>
2455 <option value="yes">Provide restricted gene list</option>
2456 </param>
2457 <when value="no">
2458 <param type="hidden" name="genelist6" value="-1"/>
2459 </when>
2460 <when value="yes">
2461 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2462 </when>
2463 </conditional>
2464 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2465 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2466 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2467 <!-- END: 9 samples, no refpairs, entry 6-->
2468 <!-- START: 9 samples, no refpairs, entry 7-->
2469 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2470 <param type="hidden" name="reffile7" value="na"/>
2471 <conditional name="genelist7">
2472 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2473 <option value="no">Plot whole genome</option>
2474 <option value="yes">Provide restricted gene list</option>
2475 </param>
2476 <when value="no">
2477 <param type="hidden" name="genelist7" value="-1"/>
2478 </when>
2479 <when value="yes">
2480 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2481 </when>
2482 </conditional>
2483 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2484 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2485 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2486 <!-- END: 9 samples, no refpairs, entry 7-->
2487 <!-- START: 9 samples, no refpairs, entry 8-->
2488 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2489 <param type="hidden" name="reffile8" value="na"/>
2490 <conditional name="genelist8">
2491 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2492 <option value="no">Plot whole genome</option>
2493 <option value="yes">Provide restricted gene list</option>
2494 </param>
2495 <when value="no">
2496 <param type="hidden" name="genelist8" value="-1"/>
2497 </when>
2498 <when value="yes">
2499 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2500 </when>
2501 </conditional>
2502 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2503 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2504 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2505 <!-- END: 9 samples, no refpairs, entry 8-->
2506 <!-- START: 9 samples, no refpairs, entry 9-->
2507 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
2508 <param type="hidden" name="reffile9" value="na"/>
2509 <conditional name="genelist9">
2510 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
2511 <option value="no">Plot whole genome</option>
2512 <option value="yes">Provide restricted gene list</option>
2513 </param>
2514 <when value="no">
2515 <param type="hidden" name="genelist9" value="-1"/>
2516 </when>
2517 <when value="yes">
2518 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
2519 </when>
2520 </conditional>
2521 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
2522 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
2523 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
2524 <!-- END: 9 samples, no refpairs, entry 9-->
2525 </when>
2526 <when value="yes">
2527 <!-- START: 9 samples, yes refpairs, entry 1-->
2528 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2529 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
2530 <conditional name="genelist1">
2531 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2532 <option value="no">Plot whole genome</option>
2533 <option value="yes">Provide restricted gene list</option>
2534 </param>
2535 <when value="no">
2536 <param type="hidden" name="genelist1" value="-1"/>
2537 </when>
2538 <when value="yes">
2539 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2540 </when>
2541 </conditional>
2542 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2543 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2544 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2545 <!-- END: 9 samples, yes refpairs, entry 1-->
2546 <!-- START: 9 samples, yes refpairs, entry 2-->
2547 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2548 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
2549 <conditional name="genelist2">
2550 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2551 <option value="no">Plot whole genome</option>
2552 <option value="yes">Provide restricted gene list</option>
2553 </param>
2554 <when value="no">
2555 <param type="hidden" name="genelist2" value="-1"/>
2556 </when>
2557 <when value="yes">
2558 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2559 </when>
2560 </conditional>
2561 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2562 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2563 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2564 <!-- END: 9 samples, yes refpairs, entry 2-->
2565 <!-- START: 9 samples, yes refpairs, entry 3-->
2566 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2567 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
2568 <conditional name="genelist3">
2569 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2570 <option value="no">Plot whole genome</option>
2571 <option value="yes">Provide restricted gene list</option>
2572 </param>
2573 <when value="no">
2574 <param type="hidden" name="genelist3" value="-1"/>
2575 </when>
2576 <when value="yes">
2577 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2578 </when>
2579 </conditional>
2580 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2581 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2582 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2583 <!-- END: 9 samples, yes refpairs, entry 3-->
2584 <!-- START: 9 samples, yes refpairs, entry 4-->
2585 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2586 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
2587 <conditional name="genelist4">
2588 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2589 <option value="no">Plot whole genome</option>
2590 <option value="yes">Provide restricted gene list</option>
2591 </param>
2592 <when value="no">
2593 <param type="hidden" name="genelist4" value="-1"/>
2594 </when>
2595 <when value="yes">
2596 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2597 </when>
2598 </conditional>
2599 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2600 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2601 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2602 <!-- END: 9 samples, yes refpairs, entry 4-->
2603 <!-- START: 9 samples, yes refpairs, entry 5-->
2604 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2605 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
2606 <conditional name="genelist5">
2607 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2608 <option value="no">Plot whole genome</option>
2609 <option value="yes">Provide restricted gene list</option>
2610 </param>
2611 <when value="no">
2612 <param type="hidden" name="genelist5" value="-1"/>
2613 </when>
2614 <when value="yes">
2615 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2616 </when>
2617 </conditional>
2618 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2619 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2620 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2621 <!-- END: 9 samples, yes refpairs, entry 5-->
2622 <!-- START: 9 samples, yes refpairs, entry 6-->
2623 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2624 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
2625 <conditional name="genelist6">
2626 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2627 <option value="no">Plot whole genome</option>
2628 <option value="yes">Provide restricted gene list</option>
2629 </param>
2630 <when value="no">
2631 <param type="hidden" name="genelist6" value="-1"/>
2632 </when>
2633 <when value="yes">
2634 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2635 </when>
2636 </conditional>
2637 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2638 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2639 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2640 <!-- END: 9 samples, yes refpairs, entry 6-->
2641 <!-- START: 9 samples, yes refpairs, entry 7-->
2642 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2643 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
2644 <conditional name="genelist7">
2645 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2646 <option value="no">Plot whole genome</option>
2647 <option value="yes">Provide restricted gene list</option>
2648 </param>
2649 <when value="no">
2650 <param type="hidden" name="genelist7" value="-1"/>
2651 </when>
2652 <when value="yes">
2653 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2654 </when>
2655 </conditional>
2656 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2657 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2658 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2659 <!-- END: 9 samples, yes refpairs, entry 7-->
2660 <!-- START: 9 samples, yes refpairs, entry 8-->
2661 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2662 <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/>
2663 <conditional name="genelist8">
2664 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2665 <option value="no">Plot whole genome</option>
2666 <option value="yes">Provide restricted gene list</option>
2667 </param>
2668 <when value="no">
2669 <param type="hidden" name="genelist8" value="-1"/>
2670 </when>
2671 <when value="yes">
2672 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2673 </when>
2674 </conditional>
2675 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2676 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2677 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2678 <!-- END: 9 samples, yes refpairs, entry 8-->
2679 <!-- START: 9 samples, yes refpairs, entry 9-->
2680 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
2681 <param type="data" name="reffile9" label="Sample 9: Reference BAM file"/>
2682 <conditional name="genelist9">
2683 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
2684 <option value="no">Plot whole genome</option>
2685 <option value="yes">Provide restricted gene list</option>
2686 </param>
2687 <when value="no">
2688 <param type="hidden" name="genelist9" value="-1"/>
2689 </when>
2690 <when value="yes">
2691 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
2692 </when>
2693 </conditional>
2694 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
2695 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
2696 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
2697 <!-- END: 9 samples, yes refpairs, entry 9-->
2698 </when>
2699 </conditional>
2700 </when>
2701 <when value="10">
2702 <conditional name="usepair">
2703 <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.">
2704 <option value="no">No</option>
2705 <option value="yes">Yes</option>
2706 </param>
2707 <when value="no">
2708 <!-- START: 10 samples, no refpairs, entry 1-->
2709 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2710 <param type="hidden" name="reffile1" value="na"/>
2711 <conditional name="genelist1">
2712 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2713 <option value="no">Plot whole genome</option>
2714 <option value="yes">Provide restricted gene list</option>
2715 </param>
2716 <when value="no">
2717 <param type="hidden" name="genelist1" value="-1"/>
2718 </when>
2719 <when value="yes">
2720 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2721 </when>
2722 </conditional>
2723 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2724 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2725 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2726 <!-- END: 10 samples, no refpairs, entry 1-->
2727 <!-- START: 10 samples, no refpairs, entry 2-->
2728 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2729 <param type="hidden" name="reffile2" value="na"/>
2730 <conditional name="genelist2">
2731 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2732 <option value="no">Plot whole genome</option>
2733 <option value="yes">Provide restricted gene list</option>
2734 </param>
2735 <when value="no">
2736 <param type="hidden" name="genelist2" value="-1"/>
2737 </when>
2738 <when value="yes">
2739 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2740 </when>
2741 </conditional>
2742 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2743 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2744 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2745 <!-- END: 10 samples, no refpairs, entry 2-->
2746 <!-- START: 10 samples, no refpairs, entry 3-->
2747 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2748 <param type="hidden" name="reffile3" value="na"/>
2749 <conditional name="genelist3">
2750 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2751 <option value="no">Plot whole genome</option>
2752 <option value="yes">Provide restricted gene list</option>
2753 </param>
2754 <when value="no">
2755 <param type="hidden" name="genelist3" value="-1"/>
2756 </when>
2757 <when value="yes">
2758 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2759 </when>
2760 </conditional>
2761 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2762 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2763 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2764 <!-- END: 10 samples, no refpairs, entry 3-->
2765 <!-- START: 10 samples, no refpairs, entry 4-->
2766 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2767 <param type="hidden" name="reffile4" value="na"/>
2768 <conditional name="genelist4">
2769 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2770 <option value="no">Plot whole genome</option>
2771 <option value="yes">Provide restricted gene list</option>
2772 </param>
2773 <when value="no">
2774 <param type="hidden" name="genelist4" value="-1"/>
2775 </when>
2776 <when value="yes">
2777 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2778 </when>
2779 </conditional>
2780 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2781 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2782 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2783 <!-- END: 10 samples, no refpairs, entry 4-->
2784 <!-- START: 10 samples, no refpairs, entry 5-->
2785 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2786 <param type="hidden" name="reffile5" value="na"/>
2787 <conditional name="genelist5">
2788 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2789 <option value="no">Plot whole genome</option>
2790 <option value="yes">Provide restricted gene list</option>
2791 </param>
2792 <when value="no">
2793 <param type="hidden" name="genelist5" value="-1"/>
2794 </when>
2795 <when value="yes">
2796 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2797 </when>
2798 </conditional>
2799 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2800 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2801 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2802 <!-- END: 10 samples, no refpairs, entry 5-->
2803 <!-- START: 10 samples, no refpairs, entry 6-->
2804 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2805 <param type="hidden" name="reffile6" value="na"/>
2806 <conditional name="genelist6">
2807 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
2808 <option value="no">Plot whole genome</option>
2809 <option value="yes">Provide restricted gene list</option>
2810 </param>
2811 <when value="no">
2812 <param type="hidden" name="genelist6" value="-1"/>
2813 </when>
2814 <when value="yes">
2815 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
2816 </when>
2817 </conditional>
2818 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
2819 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
2820 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
2821 <!-- END: 10 samples, no refpairs, entry 6-->
2822 <!-- START: 10 samples, no refpairs, entry 7-->
2823 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
2824 <param type="hidden" name="reffile7" value="na"/>
2825 <conditional name="genelist7">
2826 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
2827 <option value="no">Plot whole genome</option>
2828 <option value="yes">Provide restricted gene list</option>
2829 </param>
2830 <when value="no">
2831 <param type="hidden" name="genelist7" value="-1"/>
2832 </when>
2833 <when value="yes">
2834 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
2835 </when>
2836 </conditional>
2837 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
2838 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
2839 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
2840 <!-- END: 10 samples, no refpairs, entry 7-->
2841 <!-- START: 10 samples, no refpairs, entry 8-->
2842 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
2843 <param type="hidden" name="reffile8" value="na"/>
2844 <conditional name="genelist8">
2845 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
2846 <option value="no">Plot whole genome</option>
2847 <option value="yes">Provide restricted gene list</option>
2848 </param>
2849 <when value="no">
2850 <param type="hidden" name="genelist8" value="-1"/>
2851 </when>
2852 <when value="yes">
2853 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
2854 </when>
2855 </conditional>
2856 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
2857 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
2858 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
2859 <!-- END: 10 samples, no refpairs, entry 8-->
2860 <!-- START: 10 samples, no refpairs, entry 9-->
2861 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
2862 <param type="hidden" name="reffile9" value="na"/>
2863 <conditional name="genelist9">
2864 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
2865 <option value="no">Plot whole genome</option>
2866 <option value="yes">Provide restricted gene list</option>
2867 </param>
2868 <when value="no">
2869 <param type="hidden" name="genelist9" value="-1"/>
2870 </when>
2871 <when value="yes">
2872 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
2873 </when>
2874 </conditional>
2875 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
2876 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
2877 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
2878 <!-- END: 10 samples, no refpairs, entry 9-->
2879 <!-- START: 10 samples, no refpairs, entry 10-->
2880 <param type="data" name="bamfile10" label="Sample 10: Input BAM file"/>
2881 <param type="hidden" name="reffile10" value="na"/>
2882 <conditional name="genelist10">
2883 <param type="select" name="usegenelist10" label="Sample 10: Gene list">
2884 <option value="no">Plot whole genome</option>
2885 <option value="yes">Provide restricted gene list</option>
2886 </param>
2887 <when value="no">
2888 <param type="hidden" name="genelist10" value="-1"/>
2889 </when>
2890 <when value="yes">
2891 <param type="data" name="genelist10" label="Choose the uploaded gene list for plotting"/>
2892 </when>
2893 </conditional>
2894 <param type="text" name="title10" value="plot10" label="Sample 10: Image title"/>
2895 <param type="text" name="fraglen10" value="150" label="Sample 10: Expected fragment length"/>
2896 <param type="text" name="linecol10" value="tan3" label="Sample 10: Line plot color"/>
2897 <!-- END: 10 samples, no refpairs, entry 10-->
2898 </when>
2899 <when value="yes">
2900 <!-- START: 10 samples, yes refpairs, entry 1-->
2901 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
2902 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
2903 <conditional name="genelist1">
2904 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
2905 <option value="no">Plot whole genome</option>
2906 <option value="yes">Provide restricted gene list</option>
2907 </param>
2908 <when value="no">
2909 <param type="hidden" name="genelist1" value="-1"/>
2910 </when>
2911 <when value="yes">
2912 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
2913 </when>
2914 </conditional>
2915 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
2916 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
2917 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
2918 <!-- END: 10 samples, yes refpairs, entry 1-->
2919 <!-- START: 10 samples, yes refpairs, entry 2-->
2920 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
2921 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
2922 <conditional name="genelist2">
2923 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
2924 <option value="no">Plot whole genome</option>
2925 <option value="yes">Provide restricted gene list</option>
2926 </param>
2927 <when value="no">
2928 <param type="hidden" name="genelist2" value="-1"/>
2929 </when>
2930 <when value="yes">
2931 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
2932 </when>
2933 </conditional>
2934 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
2935 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
2936 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
2937 <!-- END: 10 samples, yes refpairs, entry 2-->
2938 <!-- START: 10 samples, yes refpairs, entry 3-->
2939 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
2940 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
2941 <conditional name="genelist3">
2942 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
2943 <option value="no">Plot whole genome</option>
2944 <option value="yes">Provide restricted gene list</option>
2945 </param>
2946 <when value="no">
2947 <param type="hidden" name="genelist3" value="-1"/>
2948 </when>
2949 <when value="yes">
2950 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
2951 </when>
2952 </conditional>
2953 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
2954 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
2955 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
2956 <!-- END: 10 samples, yes refpairs, entry 3-->
2957 <!-- START: 10 samples, yes refpairs, entry 4-->
2958 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
2959 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
2960 <conditional name="genelist4">
2961 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
2962 <option value="no">Plot whole genome</option>
2963 <option value="yes">Provide restricted gene list</option>
2964 </param>
2965 <when value="no">
2966 <param type="hidden" name="genelist4" value="-1"/>
2967 </when>
2968 <when value="yes">
2969 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
2970 </when>
2971 </conditional>
2972 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
2973 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
2974 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
2975 <!-- END: 10 samples, yes refpairs, entry 4-->
2976 <!-- START: 10 samples, yes refpairs, entry 5-->
2977 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
2978 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
2979 <conditional name="genelist5">
2980 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
2981 <option value="no">Plot whole genome</option>
2982 <option value="yes">Provide restricted gene list</option>
2983 </param>
2984 <when value="no">
2985 <param type="hidden" name="genelist5" value="-1"/>
2986 </when>
2987 <when value="yes">
2988 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
2989 </when>
2990 </conditional>
2991 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
2992 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
2993 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
2994 <!-- END: 10 samples, yes refpairs, entry 5-->
2995 <!-- START: 10 samples, yes refpairs, entry 6-->
2996 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
2997 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
2998 <conditional name="genelist6">
2999 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
3000 <option value="no">Plot whole genome</option>
3001 <option value="yes">Provide restricted gene list</option>
3002 </param>
3003 <when value="no">
3004 <param type="hidden" name="genelist6" value="-1"/>
3005 </when>
3006 <when value="yes">
3007 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
3008 </when>
3009 </conditional>
3010 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
3011 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
3012 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
3013 <!-- END: 10 samples, yes refpairs, entry 6-->
3014 <!-- START: 10 samples, yes refpairs, entry 7-->
3015 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
3016 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
3017 <conditional name="genelist7">
3018 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
3019 <option value="no">Plot whole genome</option>
3020 <option value="yes">Provide restricted gene list</option>
3021 </param>
3022 <when value="no">
3023 <param type="hidden" name="genelist7" value="-1"/>
3024 </when>
3025 <when value="yes">
3026 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
3027 </when>
3028 </conditional>
3029 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
3030 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
3031 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
3032 <!-- END: 10 samples, yes refpairs, entry 7-->
3033 <!-- START: 10 samples, yes refpairs, entry 8-->
3034 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
3035 <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/>
3036 <conditional name="genelist8">
3037 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
3038 <option value="no">Plot whole genome</option>
3039 <option value="yes">Provide restricted gene list</option>
3040 </param>
3041 <when value="no">
3042 <param type="hidden" name="genelist8" value="-1"/>
3043 </when>
3044 <when value="yes">
3045 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
3046 </when>
3047 </conditional>
3048 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
3049 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
3050 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
3051 <!-- END: 10 samples, yes refpairs, entry 8-->
3052 <!-- START: 10 samples, yes refpairs, entry 9-->
3053 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
3054 <param type="data" name="reffile9" label="Sample 9: Reference BAM file"/>
3055 <conditional name="genelist9">
3056 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
3057 <option value="no">Plot whole genome</option>
3058 <option value="yes">Provide restricted gene list</option>
3059 </param>
3060 <when value="no">
3061 <param type="hidden" name="genelist9" value="-1"/>
3062 </when>
3063 <when value="yes">
3064 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
3065 </when>
3066 </conditional>
3067 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
3068 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
3069 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
3070 <!-- END: 10 samples, yes refpairs, entry 9-->
3071 <!-- START: 10 samples, yes refpairs, entry 10-->
3072 <param type="data" name="bamfile10" label="Sample 10: Input BAM file"/>
3073 <param type="data" name="reffile10" label="Sample 10: Reference BAM file"/>
3074 <conditional name="genelist10">
3075 <param type="select" name="usegenelist10" label="Sample 10: Gene list">
3076 <option value="no">Plot whole genome</option>
3077 <option value="yes">Provide restricted gene list</option>
3078 </param>
3079 <when value="no">
3080 <param type="hidden" name="genelist10" value="-1"/>
3081 </when>
3082 <when value="yes">
3083 <param type="data" name="genelist10" label="Choose the uploaded gene list for plotting"/>
3084 </when>
3085 </conditional>
3086 <param type="text" name="title10" value="plot10" label="Sample 10: Image title"/>
3087 <param type="text" name="fraglen10" value="150" label="Sample 10: Expected fragment length"/>
3088 <param type="text" name="linecol10" value="tan3" label="Sample 10: Line plot color"/>
3089 <!-- END: 10 samples, yes refpairs, entry 10-->
3090 </when>
3091 </conditional>
3092 </when>
3093 </conditional>
3094
3095
3096
3097 <param type="select" name="gene_database" label="Supported gene database: RefSeq, Ensembl">
3098 <option value="ensembl">Ensembl</option>
3099 <option value="refseq">RefSeq</option>
3100 </param>
3101 <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."/>
3102 <conditional name="GO">
3103 <param type="select" name="gene_order" label="Gene order algorithm">
3104 <option value="total">Overall enrichment of the 1st profile</option>
3105 <option value="hc">Hierarchical clustering</option>
3106 <option value="max">Peak value of the 1st profile</option>
3107 <option value="prod">Product of all profiles on the same region</option>
3108 <option value="diff">Difference between the 1st and 2nd profiles</option>
3109 <option value="km">K-means clustering</option>
3110 <option value="none">No ranking algorithm applied. Use order in gene list.</option>
3111 </param>
3112 <when value="km">
3113 <param type="text" name="KNC" value="5" label="K-means: Number of clusters" help=""/>
3114 <param type="text" name="MIT" value="20" label="K-means: Number of iterations" help=""/>
3115 <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."/>
3116 </when>
3117 <when value="total">
3118 <param type="hidden" name="KNC" value="NA" />
3119 <param type="hidden" name="MIT" value="NA" />
3120 <param type="hidden" name="NRS" value="NA" />
3121 </when>
3122 <when value="hc">
3123 <param type="hidden" name="KNC" value="NA" />
3124 <param type="hidden" name="MIT" value="NA" />
3125 <param type="hidden" name="NRS" value="NA" />
3126 </when>
3127 <when value="max">
3128 <param type="hidden" name="KNC" value="NA" />
3129 <param type="hidden" name="MIT" value="NA" />
3130 <param type="hidden" name="NRS" value="NA" />
3131 </when>
3132 <when value="prod">
3133 <param type="hidden" name="KNC" value="NA" />
3134 <param type="hidden" name="MIT" value="NA" />
3135 <param type="hidden" name="NRS" value="NA" />
3136 </when>
3137 <when value="diff">
3138 <param type="hidden" name="KNC" value="NA" />
3139 <param type="hidden" name="MIT" value="NA" />
3140 <param type="hidden" name="NRS" value="NA" />
3141 </when>
3142 <when value="none">
3143 <param type="hidden" name="KNC" value="NA" />
3144 <param type="hidden" name="MIT" value="NA" />
3145 <param type="hidden" name="NRS" value="NA" />
3146 </when>
3147 </conditional>
3148 <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."/>
3149 <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%."/>
3150 <param type="select" name="standard_error" label="Plot standard errors" help="Standard errors will be rendered as shaded area around each curve.">
3151 <option value="1">Yes</option>
3152 <option value="0">No</option>
3153 </param>
3154
3155 <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."/>
3156 <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."/>
3157 <param type="select" name="smooth_method" label="Moving window width to smooth avg. profiles">
3158 <option value="1">No</option>
3159 <option value="3">Slightly</option>
3160 <option value="5">Somewhat</option>
3161 <option value="9">Quite</option>
3162 <option value="13">Super</option>
3163 </param>
3164 <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."/>
3165 <!--
3166 -->
3167 </inputs>
3168
3169 <help></help>
3170 <outputs>
3171 <data format="pdf" name="out_avg_png" />
3172 <data format="pdf" name="out_hm_png" />
3173 <data format="zip" name="out_zip"/>
3174 </outputs>
3175 </tool>