Mercurial > repos > ngsplot > ngsplot
comparison ngsplot_galaxytoolshed_v.10/ngsplot_main/ngsplot.xml @ 12:f7debdafc7cb draft default tip
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author | ngsplot |
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date | Tue, 31 Mar 2015 10:15:27 -0400 |
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11:896dfca167fb | 12:f7debdafc7cb |
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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> |