Mercurial > repos > galaxyp > proteomiqon_labeledproteinquantification
comparison labeledproteinquantification.xml @ 0:cbdfdca98db3 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification commit eda2d62c81b38ed3975482d0198e3dd75ff1d74f"
author | galaxyp |
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date | Thu, 16 Sep 2021 21:11:34 +0000 |
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-1:000000000000 | 0:cbdfdca98db3 |
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1 <tool id="proteomiqon_labeledproteinquantification" name="Proteomiqon LabeledProteinQuantification" version="@VERSION@" profile="20.05"> | |
2 <description> | |
3 estimates protein abundances using quantified peptide ions. | |
4 </description> | |
5 <macros> | |
6 <token name="@VERSION@">0.0.1</token> | |
7 <import>aggregationparams.xml</import> | |
8 </macros> | |
9 <requirements> | |
10 <requirement type="package" version="@VERSION@">proteomiqon-labeledproteinquantification</requirement> | |
11 </requirements> | |
12 <command detect_errors="exit_code"><![CDATA[ | |
13 #import re | |
14 #for $quantAndProtFile in $proteinassignedquantpepions | |
15 #set basename = $re.sub(r'[^\w ,.\-+]','_',$quantAndProtFile.element_identifier) | |
16 ln -s '$quantAndProtFile' '${basename}.quantAndProt' && | |
17 #end for | |
18 #if $outputParamfile: | |
19 cat '$paramfile' >> '$out_paramfile' && | |
20 #end if | |
21 ln -s '$out_labeledQuant' 'LabeledQuant.txt' && | |
22 proteomiqon-labeledproteinquantification -i './' -p '$paramfile' -o './' | |
23 ]]> | |
24 </command> | |
25 <configfiles> | |
26 <configfile name="paramfile"> | |
27 <![CDATA[ | |
28 { | |
29 #if $CorrelationLightHeavyThreshold | |
30 "Correlation_Light_Heavy_Threshold": { | |
31 "Case": "Some", | |
32 "Fields": [ | |
33 ${CorrelationLightHeavyThreshold} | |
34 ] | |
35 }, | |
36 #else | |
37 "Correlation_Light_Heavy_Threshold": null, | |
38 #end if | |
39 "ModificationFilter": { | |
40 "Case": "${ModificationFilterCond.ModificationFilter}", | |
41 #if $ModificationFilterCond.ModificationFilter == "UseOnly" | |
42 "Fields": [ | |
43 [ | |
44 #for $mod in $ModificationFilterCond.ModificationFilterSequence | |
45 { | |
46 "Case": "${mod}" | |
47 }, | |
48 #end for | |
49 ] | |
50 ] | |
51 #end if | |
52 }, | |
53 "AggregateGlobalModificationsParams": { | |
54 #set $aggregationParams = $GlobalAggregationParams | |
55 #set $labeledTransformSection = $aggregationParams.LabeledTransform | |
56 #set $labeledTransformLight = $labeledTransformSection.LabeledTransformLightCond | |
57 #set $labeledTransformHeavy = $labeledTransformSection.LabeledTransformHeavyCond | |
58 #set $labeledTransformRatio = $labeledTransformSection.LabeledTransformRatioCond | |
59 #if $labeledTransformLight.Type == "None" and $labeledTransformHeavy.Type == "None" and $labeledTransformRatio.Type == "None" | |
60 "LabeledTransform": null, | |
61 #else | |
62 "LabeledTransform": { | |
63 "Case": "Some", | |
64 "Fields": [ | |
65 { | |
66 #if $labeledTransformLight.Type == "None" | |
67 "Light": null, | |
68 #else | |
69 "Light": { | |
70 "Case": "Some", | |
71 "Fields": [ | |
72 { | |
73 "Case": "${labeledTransformLight.Type}", | |
74 #if $labeledTransformLight.Type != "Log2" | |
75 "Fields": [ | |
76 $labeledTransformLight.Value | |
77 ] | |
78 #end if | |
79 } | |
80 ] | |
81 }, | |
82 #end if | |
83 #if $labeledTransformHeavy.Type == "None" | |
84 "Heavy": null, | |
85 #else | |
86 "Heavy": { | |
87 "Case": "Some", | |
88 "Fields": [ | |
89 { | |
90 "Case": "${labeledTransformHeavy.Type}", | |
91 #if $labeledTransformHeavy.Type != "Log2" | |
92 "Fields": [ | |
93 $labeledTransformHeavy.Value | |
94 ] | |
95 #end if | |
96 } | |
97 ] | |
98 }, | |
99 #end if | |
100 #if $labeledTransformRatio.Type == "None" | |
101 "Ratio": null | |
102 #else | |
103 "Ratio": { | |
104 "Case": "Some", | |
105 "Fields": [ | |
106 { | |
107 "Case": "${labeledTransformRatio.Type}", | |
108 #if $labeledTransformRatio.Type != "Log2" | |
109 "Fields": [ | |
110 $labeledTransformRatio.Value | |
111 ] | |
112 #end if | |
113 } | |
114 ] | |
115 } | |
116 #end if | |
117 } | |
118 ] | |
119 }, | |
120 #end if | |
121 #set $labeledSingleFiltersSection = $aggregationParams.LabeledSingleFilters | |
122 #set $labeledSingleFiltersLight = $labeledSingleFiltersSection.Light | |
123 #set $labeledSingleFiltersHeavy = $labeledSingleFiltersSection.Heavy | |
124 #set $labeledSingleFiltersRatio = $labeledSingleFiltersSection.Ratio | |
125 #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan and \ | |
126 not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan and \ | |
127 not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan | |
128 "LabeledSingleFilters": null, | |
129 #else | |
130 "LabeledSingleFilters": { | |
131 "Case": "Some", | |
132 "Fields": [ | |
133 { | |
134 #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan | |
135 "Light": null, | |
136 #else | |
137 "Light": { | |
138 "Case": "Some", | |
139 "Fields": [ | |
140 [ | |
141 #if $labeledSingleFiltersLight.BiggerThan | |
142 { | |
143 "Case": "IsBiggerThan", | |
144 "Fields": [ | |
145 $labeledSingleFiltersLight.BiggerThan | |
146 ] | |
147 }, | |
148 #end if | |
149 #if $labeledSingleFiltersLight.SmallerThan | |
150 { | |
151 "Case": "IsSmallerThan", | |
152 "Fields": [ | |
153 $labeledSingleFiltersLight.SmallerThan | |
154 ] | |
155 } | |
156 #end if | |
157 ] | |
158 ] | |
159 }, | |
160 #end if | |
161 #if not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan | |
162 "Heavy": null, | |
163 #else | |
164 "Heavy": { | |
165 "Case": "Some", | |
166 "Fields": [ | |
167 [ | |
168 #if $labeledSingleFiltersHeavy.BiggerThan | |
169 { | |
170 "Case": "IsBiggerThan", | |
171 "Fields": [ | |
172 $labeledSingleFiltersHeavy.BiggerThan | |
173 ] | |
174 }, | |
175 #end if | |
176 #if $labeledSingleFiltersHeavy.SmallerThan | |
177 { | |
178 "Case": "IsSmallerThan", | |
179 "Fields": [ | |
180 $labeledSingleFiltersHeavy.SmallerThan | |
181 ] | |
182 } | |
183 #end if | |
184 ] | |
185 ] | |
186 }, | |
187 #end if | |
188 #if not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan | |
189 "Ratio": null | |
190 #else | |
191 "Ratio": { | |
192 "Case": "Some", | |
193 "Fields": [ | |
194 [ | |
195 #if $labeledSingleFiltersRatio.BiggerThan | |
196 { | |
197 "Case": "IsBiggerThan", | |
198 "Fields": [ | |
199 $labeledSingleFiltersRatio.BiggerThan | |
200 ] | |
201 }, | |
202 #end if | |
203 #if $labeledSingleFiltersRatio.SmallerThan | |
204 { | |
205 "Case": "IsSmallerThan", | |
206 "Fields": [ | |
207 $labeledSingleFiltersRatio.SmallerThan | |
208 ] | |
209 } | |
210 #end if | |
211 ] | |
212 ] | |
213 } | |
214 #end if | |
215 } | |
216 ] | |
217 }, | |
218 #end if | |
219 #set $labeledGroupFiltersSection = $aggregationParams.LabeledGroupFilters | |
220 #set $labeledGroupFiltersLight = $labeledGroupFiltersSection.Light | |
221 #set $labeledGroupFiltersHeavy = $labeledGroupFiltersSection.Heavy | |
222 #set $labeledGroupFiltersRatio = $labeledGroupFiltersSection.Ratio | |
223 #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev and \ | |
224 not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev and \ | |
225 not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev | |
226 "LabeledGroupFilters": null, | |
227 #else | |
228 "LabeledGroupFilters": { | |
229 "Case": "Some", | |
230 "Fields": [ | |
231 { | |
232 | |
233 | |
234 #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev | |
235 "Light": null, | |
236 #else | |
237 "Light": { | |
238 "Case": "Some", | |
239 "Fields": [ | |
240 [ | |
241 #if $labeledGroupFiltersLight.Tukey | |
242 { | |
243 "Case": "Tukey", | |
244 "Fields": [ | |
245 $labeledGroupFiltersLight.Tukey | |
246 ] | |
247 }, | |
248 #end if | |
249 #if $labeledGroupFiltersLight.Stdev | |
250 { | |
251 "Case": "Stdev", | |
252 "Fields": [ | |
253 $labeledGroupFiltersLight.Stdev | |
254 ] | |
255 } | |
256 #end if | |
257 ] | |
258 ] | |
259 }, | |
260 #end if | |
261 #if not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev | |
262 "Heavy": null, | |
263 #else | |
264 "Heavy": { | |
265 "Case": "Some", | |
266 "Fields": [ | |
267 [ | |
268 #if $labeledGroupFiltersHeavy.Tukey | |
269 { | |
270 "Case": "Tukey", | |
271 "Fields": [ | |
272 $labeledGroupFiltersHeavy.Tukey | |
273 ] | |
274 }, | |
275 #end if | |
276 #if $labeledGroupFiltersHeavy.Stdev | |
277 { | |
278 "Case": "Stdev", | |
279 "Fields": [ | |
280 $labeledGroupFiltersHeavy.Stdev | |
281 ] | |
282 } | |
283 #end if | |
284 ] | |
285 ] | |
286 }, | |
287 #end if | |
288 #if not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev | |
289 "Ratio": null | |
290 #else | |
291 "Ratio": { | |
292 "Case": "Some", | |
293 "Fields": [ | |
294 [ | |
295 #if $labeledGroupFiltersRatio.Tukey | |
296 { | |
297 "Case": "Tukey", | |
298 "Fields": [ | |
299 $labeledGroupFiltersRatio.Tukey | |
300 ] | |
301 }, | |
302 #end if | |
303 #if $labeledGroupFiltersRatio.Stdev | |
304 { | |
305 "Case": "Stdev", | |
306 "Fields": [ | |
307 $labeledGroupFiltersRatio.Stdev | |
308 ] | |
309 } | |
310 #end if | |
311 ] | |
312 ] | |
313 } | |
314 #end if | |
315 } | |
316 ] | |
317 }, | |
318 #end if | |
319 "LabeledAggregation": { | |
320 "Light": { | |
321 "Case": "${aggregationParams.LabeledAggregation.labeledAggregationLight}" | |
322 }, | |
323 "Heavy": { | |
324 "Case": "${aggregationParams.LabeledAggregation.labeledAggregationHeavy}" | |
325 }, | |
326 "Ratio": { | |
327 "Case": "${aggregationParams.LabeledAggregation.labeledAggregationRatio}" | |
328 } | |
329 } | |
330 }, | |
331 #set $aggregationParams = $AggregatePeptideChargeStatesParams.AggregatePeptideChargeStatesParamsCond | |
332 #if $aggregationParams.AggregatePeptideChargeStatesParamsEnabled == "no" | |
333 "AggregatePeptideChargeStatesParams": null, | |
334 #else | |
335 "AggregatePeptideChargeStatesParams": { | |
336 "Case": "Some", | |
337 "Fields": [ | |
338 { | |
339 #set $labeledTransformSection = $aggregationParams.LabeledTransform | |
340 #set $labeledTransformLight = $labeledTransformSection.LabeledTransformLightCond | |
341 #set $labeledTransformHeavy = $labeledTransformSection.LabeledTransformHeavyCond | |
342 #set $labeledTransformRatio = $labeledTransformSection.LabeledTransformRatioCond | |
343 #if $labeledTransformLight.Type == "None" and $labeledTransformHeavy.Type == "None" and $labeledTransformRatio.Type == "None" | |
344 "LabeledTransform": null, | |
345 #else | |
346 "LabeledTransform": { | |
347 "Case": "Some", | |
348 "Fields": [ | |
349 { | |
350 #if $labeledTransformLight.Type == "None" | |
351 "Light": null, | |
352 #else | |
353 "Light": { | |
354 "Case": "Some", | |
355 "Fields": [ | |
356 { | |
357 "Case": "${labeledTransformLight.Type}", | |
358 #if $labeledTransformLight.Type != "Log2" | |
359 "Fields": [ | |
360 $labeledTransformLight.Value | |
361 ] | |
362 #end if | |
363 } | |
364 ] | |
365 }, | |
366 #end if | |
367 #if $labeledTransformHeavy.Type == "None" | |
368 "Heavy": null, | |
369 #else | |
370 "Heavy": { | |
371 "Case": "Some", | |
372 "Fields": [ | |
373 { | |
374 "Case": "${labeledTransformHeavy.Type}", | |
375 #if $labeledTransformHeavy.Type != "Log2" | |
376 "Fields": [ | |
377 $labeledTransformHeavy.Value | |
378 ] | |
379 #end if | |
380 } | |
381 ] | |
382 }, | |
383 #end if | |
384 #if $labeledTransformRatio.Type == "None" | |
385 "Ratio": null | |
386 #else | |
387 "Ratio": { | |
388 "Case": "Some", | |
389 "Fields": [ | |
390 { | |
391 "Case": "${labeledTransformRatio.Type}", | |
392 #if $labeledTransformRatio.Type != "Log2" | |
393 "Fields": [ | |
394 $labeledTransformRatio.Value | |
395 ] | |
396 #end if | |
397 } | |
398 ] | |
399 } | |
400 #end if | |
401 } | |
402 ] | |
403 }, | |
404 #end if | |
405 #set $labeledSingleFiltersSection = $aggregationParams.LabeledSingleFilters | |
406 #set $labeledSingleFiltersLight = $labeledSingleFiltersSection.Light | |
407 #set $labeledSingleFiltersHeavy = $labeledSingleFiltersSection.Heavy | |
408 #set $labeledSingleFiltersRatio = $labeledSingleFiltersSection.Ratio | |
409 #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan and \ | |
410 not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan and \ | |
411 not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan | |
412 "LabeledSingleFilters": null, | |
413 #else | |
414 "LabeledSingleFilters": { | |
415 "Case": "Some", | |
416 "Fields": [ | |
417 { | |
418 #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan | |
419 "Light": null, | |
420 #else | |
421 "Light": { | |
422 "Case": "Some", | |
423 "Fields": [ | |
424 [ | |
425 #if $labeledSingleFiltersLight.BiggerThan | |
426 { | |
427 "Case": "IsBiggerThan", | |
428 "Fields": [ | |
429 $labeledSingleFiltersLight.BiggerThan | |
430 ] | |
431 }, | |
432 #end if | |
433 #if $labeledSingleFiltersLight.SmallerThan | |
434 { | |
435 "Case": "IsSmallerThan", | |
436 "Fields": [ | |
437 $labeledSingleFiltersLight.SmallerThan | |
438 ] | |
439 } | |
440 #end if | |
441 ] | |
442 ] | |
443 }, | |
444 #end if | |
445 #if not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan | |
446 "Heavy": null, | |
447 #else | |
448 "Heavy": { | |
449 "Case": "Some", | |
450 "Fields": [ | |
451 [ | |
452 #if $labeledSingleFiltersHeavy.BiggerThan | |
453 { | |
454 "Case": "IsBiggerThan", | |
455 "Fields": [ | |
456 $labeledSingleFiltersHeavy.BiggerThan | |
457 ] | |
458 }, | |
459 #end if | |
460 #if $labeledSingleFiltersHeavy.SmallerThan | |
461 { | |
462 "Case": "IsSmallerThan", | |
463 "Fields": [ | |
464 $labeledSingleFiltersHeavy.SmallerThan | |
465 ] | |
466 } | |
467 #end if | |
468 ] | |
469 ] | |
470 }, | |
471 #end if | |
472 #if not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan | |
473 "Ratio": null | |
474 #else | |
475 "Ratio": { | |
476 "Case": "Some", | |
477 "Fields": [ | |
478 [ | |
479 #if $labeledSingleFiltersRatio.BiggerThan | |
480 { | |
481 "Case": "IsBiggerThan", | |
482 "Fields": [ | |
483 $labeledSingleFiltersRatio.BiggerThan | |
484 ] | |
485 }, | |
486 #end if | |
487 #if $labeledSingleFiltersRatio.SmallerThan | |
488 { | |
489 "Case": "IsSmallerThan", | |
490 "Fields": [ | |
491 $labeledSingleFiltersRatio.SmallerThan | |
492 ] | |
493 } | |
494 #end if | |
495 ] | |
496 ] | |
497 } | |
498 #end if | |
499 } | |
500 ] | |
501 }, | |
502 #end if | |
503 #set $labeledGroupFiltersSection = $aggregationParams.LabeledGroupFilters | |
504 #set $labeledGroupFiltersLight = $labeledGroupFiltersSection.Light | |
505 #set $labeledGroupFiltersHeavy = $labeledGroupFiltersSection.Heavy | |
506 #set $labeledGroupFiltersRatio = $labeledGroupFiltersSection.Ratio | |
507 #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev and \ | |
508 not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev and \ | |
509 not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev | |
510 "LabeledGroupFilters": null, | |
511 #else | |
512 "LabeledGroupFilters": { | |
513 "Case": "Some", | |
514 "Fields": [ | |
515 { | |
516 #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev | |
517 "Light": null, | |
518 #else | |
519 "Light": { | |
520 "Case": "Some", | |
521 "Fields": [ | |
522 [ | |
523 #if $labeledGroupFiltersLight.Tukey | |
524 { | |
525 "Case": "Tukey", | |
526 "Fields": [ | |
527 $labeledGroupFiltersLight.Tukey | |
528 ] | |
529 }, | |
530 #end if | |
531 #if $labeledGroupFiltersLight.Stdev | |
532 { | |
533 "Case": "Stdev", | |
534 "Fields": [ | |
535 $labeledGroupFiltersLight.Stdev | |
536 ] | |
537 } | |
538 #end if | |
539 ] | |
540 ] | |
541 }, | |
542 #end if | |
543 #if not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev | |
544 "Heavy": null, | |
545 #else | |
546 "Heavy": { | |
547 "Case": "Some", | |
548 "Fields": [ | |
549 [ | |
550 #if $labeledGroupFiltersHeavy.Tukey | |
551 { | |
552 "Case": "Tukey", | |
553 "Fields": [ | |
554 $labeledGroupFiltersHeavy.Tukey | |
555 ] | |
556 }, | |
557 #end if | |
558 #if $labeledGroupFiltersHeavy.Stdev | |
559 { | |
560 "Case": "Stdev", | |
561 "Fields": [ | |
562 $labeledGroupFiltersHeavy.Stdev | |
563 ] | |
564 } | |
565 #end if | |
566 ] | |
567 ] | |
568 }, | |
569 #end if | |
570 #if not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev | |
571 "Ratio": null | |
572 #else | |
573 "Ratio": { | |
574 "Case": "Some", | |
575 "Fields": [ | |
576 [ | |
577 #if $labeledGroupFiltersRatio.Tukey | |
578 { | |
579 "Case": "Tukey", | |
580 "Fields": [ | |
581 $labeledGroupFiltersRatio.Tukey | |
582 ] | |
583 }, | |
584 #end if | |
585 #if $labeledGroupFiltersRatio.Stdev | |
586 { | |
587 "Case": "Stdev", | |
588 "Fields": [ | |
589 $labeledGroupFiltersRatio.Stdev | |
590 ] | |
591 } | |
592 #end if | |
593 ] | |
594 ] | |
595 } | |
596 #end if | |
597 } | |
598 ] | |
599 }, | |
600 #end if | |
601 "LabeledAggregation": { | |
602 "Light": { | |
603 "Case": "${aggregationParams.LabeledAggregation.labeledAggregationLight}" | |
604 }, | |
605 "Heavy": { | |
606 "Case": "${aggregationParams.LabeledAggregation.labeledAggregationHeavy}" | |
607 }, | |
608 "Ratio": { | |
609 "Case": "${aggregationParams.LabeledAggregation.labeledAggregationRatio}" | |
610 } | |
611 } | |
612 } | |
613 ] | |
614 }, | |
615 #end if | |
616 #set $aggregationParams = $AggregateModifiedPeptidesParams.AggregateModifiedPeptidesParamsCond | |
617 #if $aggregationParams.AggregateModifiedPeptidesParamsEnabled == "no" | |
618 "AggregateModifiedPeptidesParams": null, | |
619 #else | |
620 "AggregateModifiedPeptidesParams": { | |
621 "Case": "Some", | |
622 "Fields": [ | |
623 { | |
624 #set $labeledTransformSection = $aggregationParams.LabeledTransform | |
625 #set $labeledTransformLight = $labeledTransformSection.LabeledTransformLightCond | |
626 #set $labeledTransformHeavy = $labeledTransformSection.LabeledTransformHeavyCond | |
627 #set $labeledTransformRatio = $labeledTransformSection.LabeledTransformRatioCond | |
628 #if $labeledTransformLight.Type == "None" and $labeledTransformHeavy.Type == "None" and $labeledTransformRatio.Type == "None" | |
629 "LabeledTransform": null, | |
630 #else | |
631 "LabeledTransform": { | |
632 "Case": "Some", | |
633 "Fields": [ | |
634 { | |
635 #if $labeledTransformLight.Type == "None" | |
636 "Light": null, | |
637 #else | |
638 "Light": { | |
639 "Case": "Some", | |
640 "Fields": [ | |
641 { | |
642 "Case": "${labeledTransformLight.Type}", | |
643 #if $labeledTransformLight.Type != "Log2" | |
644 "Fields": [ | |
645 $labeledTransformLight.Value | |
646 ] | |
647 #end if | |
648 } | |
649 ] | |
650 }, | |
651 #end if | |
652 #if $labeledTransformHeavy.Type == "None" | |
653 "Heavy": null, | |
654 #else | |
655 "Heavy": { | |
656 "Case": "Some", | |
657 "Fields": [ | |
658 { | |
659 "Case": "${labeledTransformHeavy.Type}", | |
660 #if $labeledTransformHeavy.Type != "Log2" | |
661 "Fields": [ | |
662 $labeledTransformHeavy.Value | |
663 ] | |
664 #end if | |
665 } | |
666 ] | |
667 }, | |
668 #end if | |
669 #if $labeledTransformRatio.Type == "None" | |
670 "Ratio": null | |
671 #else | |
672 "Ratio": { | |
673 "Case": "Some", | |
674 "Fields": [ | |
675 { | |
676 "Case": "${labeledTransformRatio.Type}", | |
677 #if $labeledTransformRatio.Type != "Log2" | |
678 "Fields": [ | |
679 $labeledTransformRatio.Value | |
680 ] | |
681 #end if | |
682 } | |
683 ] | |
684 } | |
685 #end if | |
686 } | |
687 ] | |
688 }, | |
689 #end if | |
690 #set $labeledSingleFiltersSection = $aggregationParams.LabeledSingleFilters | |
691 #set $labeledSingleFiltersLight = $labeledSingleFiltersSection.Light | |
692 #set $labeledSingleFiltersHeavy = $labeledSingleFiltersSection.Heavy | |
693 #set $labeledSingleFiltersRatio = $labeledSingleFiltersSection.Ratio | |
694 #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan and \ | |
695 not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan and \ | |
696 not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan | |
697 "LabeledSingleFilters": null, | |
698 #else | |
699 "LabeledSingleFilters": { | |
700 "Case": "Some", | |
701 "Fields": [ | |
702 { | |
703 #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan | |
704 "Light": null, | |
705 #else | |
706 "Light": { | |
707 "Case": "Some", | |
708 "Fields": [ | |
709 [ | |
710 #if $labeledSingleFiltersLight.BiggerThan | |
711 { | |
712 "Case": "IsBiggerThan", | |
713 "Fields": [ | |
714 $labeledSingleFiltersLight.BiggerThan | |
715 ] | |
716 }, | |
717 #end if | |
718 #if $labeledSingleFiltersLight.SmallerThan | |
719 { | |
720 "Case": "IsSmallerThan", | |
721 "Fields": [ | |
722 $labeledSingleFiltersLight.SmallerThan | |
723 ] | |
724 } | |
725 #end if | |
726 ] | |
727 ] | |
728 }, | |
729 #end if | |
730 #if not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan | |
731 "Heavy": null, | |
732 #else | |
733 "Heavy": { | |
734 "Case": "Some", | |
735 "Fields": [ | |
736 [ | |
737 #if $labeledSingleFiltersHeavy.BiggerThan | |
738 { | |
739 "Case": "IsBiggerThan", | |
740 "Fields": [ | |
741 $labeledSingleFiltersHeavy.BiggerThan | |
742 ] | |
743 }, | |
744 #end if | |
745 #if $labeledSingleFiltersHeavy.SmallerThan | |
746 { | |
747 "Case": "IsSmallerThan", | |
748 "Fields": [ | |
749 $labeledSingleFiltersHeavy.SmallerThan | |
750 ] | |
751 } | |
752 #end if | |
753 ] | |
754 ] | |
755 }, | |
756 #end if | |
757 #if not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan | |
758 "Ratio": null | |
759 #else | |
760 "Ratio": { | |
761 "Case": "Some", | |
762 "Fields": [ | |
763 [ | |
764 #if $labeledSingleFiltersRatio.BiggerThan | |
765 { | |
766 "Case": "IsBiggerThan", | |
767 "Fields": [ | |
768 $labeledSingleFiltersRatio.BiggerThan | |
769 ] | |
770 }, | |
771 #end if | |
772 #if $labeledSingleFiltersRatio.SmallerThan | |
773 { | |
774 "Case": "IsSmallerThan", | |
775 "Fields": [ | |
776 $labeledSingleFiltersRatio.SmallerThan | |
777 ] | |
778 } | |
779 #end if | |
780 ] | |
781 ] | |
782 } | |
783 #end if | |
784 } | |
785 ] | |
786 }, | |
787 #end if | |
788 #set $labeledGroupFiltersSection = $aggregationParams.LabeledGroupFilters | |
789 #set $labeledGroupFiltersLight = $labeledGroupFiltersSection.Light | |
790 #set $labeledGroupFiltersHeavy = $labeledGroupFiltersSection.Heavy | |
791 #set $labeledGroupFiltersRatio = $labeledGroupFiltersSection.Ratio | |
792 #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev and \ | |
793 not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev and \ | |
794 not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev | |
795 "LabeledGroupFilters": null, | |
796 #else | |
797 "LabeledGroupFilters": { | |
798 "Case": "Some", | |
799 "Fields": [ | |
800 { | |
801 #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev | |
802 "Light": null, | |
803 #else | |
804 "Light": { | |
805 "Case": "Some", | |
806 "Fields": [ | |
807 [ | |
808 #if $labeledGroupFiltersLight.Tukey | |
809 { | |
810 "Case": "Tukey", | |
811 "Fields": [ | |
812 $labeledGroupFiltersLight.Tukey | |
813 ] | |
814 }, | |
815 #end if | |
816 #if $labeledGroupFiltersLight.Stdev | |
817 { | |
818 "Case": "Stdev", | |
819 "Fields": [ | |
820 $labeledGroupFiltersLight.Stdev | |
821 ] | |
822 } | |
823 #end if | |
824 ] | |
825 ] | |
826 }, | |
827 #end if | |
828 #if not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev | |
829 "Heavy": null, | |
830 #else | |
831 "Heavy": { | |
832 "Case": "Some", | |
833 "Fields": [ | |
834 [ | |
835 #if $labeledGroupFiltersHeavy.Tukey | |
836 { | |
837 "Case": "Tukey", | |
838 "Fields": [ | |
839 $labeledGroupFiltersHeavy.Tukey | |
840 ] | |
841 }, | |
842 #end if | |
843 #if $labeledGroupFiltersHeavy.Stdev | |
844 { | |
845 "Case": "Stdev", | |
846 "Fields": [ | |
847 $labeledGroupFiltersHeavy.Stdev | |
848 ] | |
849 } | |
850 #end if | |
851 ] | |
852 ] | |
853 }, | |
854 #end if | |
855 #if not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev | |
856 "Ratio": null | |
857 #else | |
858 "Ratio": { | |
859 "Case": "Some", | |
860 "Fields": [ | |
861 [ | |
862 #if $labeledGroupFiltersRatio.Tukey | |
863 { | |
864 "Case": "Tukey", | |
865 "Fields": [ | |
866 $labeledGroupFiltersRatio.Tukey | |
867 ] | |
868 }, | |
869 #end if | |
870 #if $labeledGroupFiltersRatio.Stdev | |
871 { | |
872 "Case": "Stdev", | |
873 "Fields": [ | |
874 $labeledGroupFiltersRatio.Stdev | |
875 ] | |
876 } | |
877 #end if | |
878 ] | |
879 ] | |
880 } | |
881 #end if | |
882 } | |
883 ] | |
884 }, | |
885 #end if | |
886 "LabeledAggregation": { | |
887 "Light": { | |
888 "Case": "${aggregationParams.LabeledAggregation.labeledAggregationLight}" | |
889 }, | |
890 "Heavy": { | |
891 "Case": "${aggregationParams.LabeledAggregation.labeledAggregationHeavy}" | |
892 }, | |
893 "Ratio": { | |
894 "Case": "${aggregationParams.LabeledAggregation.labeledAggregationRatio}" | |
895 } | |
896 } | |
897 } | |
898 ] | |
899 }, | |
900 #end if | |
901 "AggregateToProteinGroupsParams": { | |
902 #set $aggregationParams = $AggregateToProteinGroupsParams | |
903 #set $labeledTransformSection = $aggregationParams.LabeledTransform | |
904 #set $labeledTransformLight = $labeledTransformSection.LabeledTransformLightCond | |
905 #set $labeledTransformHeavy = $labeledTransformSection.LabeledTransformHeavyCond | |
906 #set $labeledTransformRatio = $labeledTransformSection.LabeledTransformRatioCond | |
907 #if $labeledTransformLight.Type == "None" and $labeledTransformHeavy.Type == "None" and $labeledTransformRatio.Type == "None" | |
908 "LabeledTransform": null, | |
909 #else | |
910 "LabeledTransform": { | |
911 "Case": "Some", | |
912 "Fields": [ | |
913 { | |
914 #if $labeledTransformLight.Type == "None" | |
915 "Light": null, | |
916 #else | |
917 "Light": { | |
918 "Case": "Some", | |
919 "Fields": [ | |
920 { | |
921 "Case": "${labeledTransformLight.Type}", | |
922 #if $labeledTransformLight.Type != "Log2" | |
923 "Fields": [ | |
924 $labeledTransformLight.Value | |
925 ] | |
926 #end if | |
927 } | |
928 ] | |
929 }, | |
930 #end if | |
931 #if $labeledTransformHeavy.Type == "None" | |
932 "Heavy": null, | |
933 #else | |
934 "Heavy": { | |
935 "Case": "Some", | |
936 "Fields": [ | |
937 { | |
938 "Case": "${labeledTransformHeavy.Type}", | |
939 #if $labeledTransformHeavy.Type != "Log2" | |
940 "Fields": [ | |
941 $labeledTransformHeavy.Value | |
942 ] | |
943 #end if | |
944 } | |
945 ] | |
946 }, | |
947 #end if | |
948 #if $labeledTransformRatio.Type == "None" | |
949 "Ratio": null | |
950 #else | |
951 "Ratio": { | |
952 "Case": "Some", | |
953 "Fields": [ | |
954 { | |
955 "Case": "${labeledTransformRatio.Type}", | |
956 #if $labeledTransformRatio.Type != "Log2" | |
957 "Fields": [ | |
958 $labeledTransformRatio.Value | |
959 ] | |
960 #end if | |
961 } | |
962 ] | |
963 } | |
964 #end if | |
965 } | |
966 ] | |
967 }, | |
968 #end if | |
969 #set $labeledSingleFiltersSection = $aggregationParams.LabeledSingleFilters | |
970 #set $labeledSingleFiltersLight = $labeledSingleFiltersSection.Light | |
971 #set $labeledSingleFiltersHeavy = $labeledSingleFiltersSection.Heavy | |
972 #set $labeledSingleFiltersRatio = $labeledSingleFiltersSection.Ratio | |
973 #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan and \ | |
974 not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan and \ | |
975 not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan | |
976 "LabeledSingleFilters": null, | |
977 #else | |
978 "LabeledSingleFilters": { | |
979 "Case": "Some", | |
980 "Fields": [ | |
981 { | |
982 #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan | |
983 "Light": null, | |
984 #else | |
985 "Light": { | |
986 "Case": "Some", | |
987 "Fields": [ | |
988 [ | |
989 #if $labeledSingleFiltersLight.BiggerThan | |
990 { | |
991 "Case": "IsBiggerThan", | |
992 "Fields": [ | |
993 $labeledSingleFiltersLight.BiggerThan | |
994 ] | |
995 }, | |
996 #end if | |
997 #if $labeledSingleFiltersLight.SmallerThan | |
998 { | |
999 "Case": "IsSmallerThan", | |
1000 "Fields": [ | |
1001 $labeledSingleFiltersLight.SmallerThan | |
1002 ] | |
1003 } | |
1004 #end if | |
1005 ] | |
1006 ] | |
1007 }, | |
1008 #end if | |
1009 #if not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan | |
1010 "Heavy": null, | |
1011 #else | |
1012 "Heavy": { | |
1013 "Case": "Some", | |
1014 "Fields": [ | |
1015 [ | |
1016 #if $labeledSingleFiltersHeavy.BiggerThan | |
1017 { | |
1018 "Case": "IsBiggerThan", | |
1019 "Fields": [ | |
1020 $labeledSingleFiltersHeavy.BiggerThan | |
1021 ] | |
1022 }, | |
1023 #end if | |
1024 #if $labeledSingleFiltersHeavy.SmallerThan | |
1025 { | |
1026 "Case": "IsSmallerThan", | |
1027 "Fields": [ | |
1028 $labeledSingleFiltersHeavy.SmallerThan | |
1029 ] | |
1030 } | |
1031 #end if | |
1032 ] | |
1033 ] | |
1034 }, | |
1035 #end if | |
1036 #if not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan | |
1037 "Ratio": null | |
1038 #else | |
1039 "Ratio": { | |
1040 "Case": "Some", | |
1041 "Fields": [ | |
1042 [ | |
1043 #if $labeledSingleFiltersRatio.BiggerThan | |
1044 { | |
1045 "Case": "IsBiggerThan", | |
1046 "Fields": [ | |
1047 $labeledSingleFiltersRatio.BiggerThan | |
1048 ] | |
1049 }, | |
1050 #end if | |
1051 #if $labeledSingleFiltersRatio.SmallerThan | |
1052 { | |
1053 "Case": "IsSmallerThan", | |
1054 "Fields": [ | |
1055 $labeledSingleFiltersRatio.SmallerThan | |
1056 ] | |
1057 } | |
1058 #end if | |
1059 ] | |
1060 ] | |
1061 } | |
1062 #end if | |
1063 } | |
1064 ] | |
1065 }, | |
1066 #end if | |
1067 #set $labeledGroupFiltersSection = $aggregationParams.LabeledGroupFilters | |
1068 #set $labeledGroupFiltersLight = $labeledGroupFiltersSection.Light | |
1069 #set $labeledGroupFiltersHeavy = $labeledGroupFiltersSection.Heavy | |
1070 #set $labeledGroupFiltersRatio = $labeledGroupFiltersSection.Ratio | |
1071 #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev and \ | |
1072 not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev and \ | |
1073 not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev | |
1074 "LabeledGroupFilters": null, | |
1075 #else | |
1076 "LabeledGroupFilters": { | |
1077 "Case": "Some", | |
1078 "Fields": [ | |
1079 { | |
1080 #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev | |
1081 "Light": null, | |
1082 #else | |
1083 "Light": { | |
1084 "Case": "Some", | |
1085 "Fields": [ | |
1086 [ | |
1087 #if $labeledGroupFiltersLight.Tukey | |
1088 { | |
1089 "Case": "Tukey", | |
1090 "Fields": [ | |
1091 $labeledGroupFiltersLight.Tukey | |
1092 ] | |
1093 }, | |
1094 #end if | |
1095 #if $labeledGroupFiltersLight.Stdev | |
1096 { | |
1097 "Case": "Stdev", | |
1098 "Fields": [ | |
1099 $labeledGroupFiltersLight.Stdev | |
1100 ] | |
1101 } | |
1102 #end if | |
1103 ] | |
1104 ] | |
1105 }, | |
1106 #end if | |
1107 #if not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev | |
1108 "Heavy": null, | |
1109 #else | |
1110 "Heavy": { | |
1111 "Case": "Some", | |
1112 "Fields": [ | |
1113 [ | |
1114 #if $labeledGroupFiltersHeavy.Tukey | |
1115 { | |
1116 "Case": "Tukey", | |
1117 "Fields": [ | |
1118 $labeledGroupFiltersHeavy.Tukey | |
1119 ] | |
1120 }, | |
1121 #end if | |
1122 #if $labeledGroupFiltersHeavy.Stdev | |
1123 { | |
1124 "Case": "Stdev", | |
1125 "Fields": [ | |
1126 $labeledGroupFiltersHeavy.Stdev | |
1127 ] | |
1128 } | |
1129 #end if | |
1130 ] | |
1131 ] | |
1132 }, | |
1133 #end if | |
1134 #if not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev | |
1135 "Ratio": null | |
1136 #else | |
1137 "Ratio": { | |
1138 "Case": "Some", | |
1139 "Fields": [ | |
1140 [ | |
1141 #if $labeledGroupFiltersRatio.Tukey | |
1142 { | |
1143 "Case": "Tukey", | |
1144 "Fields": [ | |
1145 $labeledGroupFiltersRatio.Tukey | |
1146 ] | |
1147 }, | |
1148 #end if | |
1149 #if $labeledGroupFiltersRatio.Stdev | |
1150 { | |
1151 "Case": "Stdev", | |
1152 "Fields": [ | |
1153 $labeledGroupFiltersRatio.Stdev | |
1154 ] | |
1155 } | |
1156 #end if | |
1157 ] | |
1158 ] | |
1159 } | |
1160 #end if | |
1161 } | |
1162 ] | |
1163 }, | |
1164 #end if | |
1165 "LabeledAggregation": { | |
1166 "Light": { | |
1167 "Case": "${aggregationParams.LabeledAggregation.labeledAggregationLight}" | |
1168 }, | |
1169 "Heavy": { | |
1170 "Case": "${aggregationParams.LabeledAggregation.labeledAggregationHeavy}" | |
1171 }, | |
1172 "Ratio": { | |
1173 "Case": "${aggregationParams.LabeledAggregation.labeledAggregationRatio}" | |
1174 } | |
1175 } | |
1176 } | |
1177 } | |
1178 ]]> | |
1179 </configfile> | |
1180 </configfiles> | |
1181 <inputs> | |
1182 <param name="proteinassignedquantpepions" type="data" format="tabular" label="Protein assigned quant pep ions" help="Specify list of .quantAndProt files" multiple="true"/> | |
1183 <param name="CorrelationLightHeavyThreshold" type="float" value="0.0" optional="true" label="Correlation Light Heavy Threshold" /> | |
1184 <conditional name="ModificationFilterCond"> | |
1185 <param name="ModificationFilter" type="select" label="Modification Filter"> | |
1186 <option value="All" selected="true">All</option> | |
1187 <option value="No">No</option> | |
1188 <option value="UseOnly">Use Only</option> | |
1189 </param> | |
1190 <when value="All"> | |
1191 </when> | |
1192 <when value="No"> | |
1193 </when> | |
1194 <when value="UseOnly"> | |
1195 <param name="ModificationFilterSequence" type="select" label="Sequence" multiple="true"> | |
1196 <option value="Acetylation'ProtNTerm'">Acetylation'ProtNTerm'</option> | |
1197 <option value="Carbamidomethyl'Cys'">Carbamidomethyl'Cys'</option> | |
1198 <option value="Oxidation'Met'">Oxidation'Met'</option> | |
1199 <option value="Phosphorylation'Ser'Thr'Tyr'">Phosphorylation'Ser'Thr'Tyr'</option> | |
1200 <option value="Pyro_Glu'GluNterm'">Pyro_Glu'GluNterm'</option> | |
1201 <option value="Pyro_Glu'GlnNterm'">Pyro_Glu'GlnNterm'</option> | |
1202 </param> | |
1203 </when> | |
1204 </conditional> | |
1205 <section name="GlobalAggregationParams" title="Aggregate Global Modifications Parameters"> | |
1206 <expand macro="AggregationParams" /> | |
1207 </section> | |
1208 <section name="AggregatePeptideChargeStatesParams" title="Aggregate Peptide Charge States Parameters"> | |
1209 <conditional name="AggregatePeptideChargeStatesParamsCond"> | |
1210 <param name="AggregatePeptideChargeStatesParamsEnabled" type="select" label="Specify Aggregate Peptide Charge States Parameters?"> | |
1211 <option value="yes">Yes</option> | |
1212 <option value="no" selected="true">No</option> | |
1213 </param> | |
1214 <when value="yes"> | |
1215 <expand macro="AggregationParams" /> | |
1216 </when> | |
1217 <when value="no"> | |
1218 </when> | |
1219 </conditional> | |
1220 </section> | |
1221 <section name="AggregateModifiedPeptidesParams" title="Aggregate Modified Peptides Parameters"> | |
1222 <conditional name="AggregateModifiedPeptidesParamsCond"> | |
1223 <param name="AggregateModifiedPeptidesParamsEnabled" type="select" label="Specify Aggregate Modified Peptides Parameters?"> | |
1224 <option value="yes">Yes</option> | |
1225 <option value="no" selected="true">No</option> | |
1226 </param> | |
1227 <when value="yes"> | |
1228 <expand macro="AggregationParams" /> | |
1229 </when> | |
1230 <when value="no"> | |
1231 </when> | |
1232 </conditional> | |
1233 </section> | |
1234 <section name="AggregateToProteinGroupsParams" title="Aggregate To Protein Groups Parameters"> | |
1235 <expand macro="AggregationParams" /> | |
1236 </section> | |
1237 <param name="outputParamfile" type="boolean" value="false" label="Output parameter file"/> | |
1238 </inputs> | |
1239 <outputs> | |
1240 <data format="tabular" name="out_labeledQuant" /> | |
1241 <data format="json" name="out_paramfile"> | |
1242 <filter>outputParamfile</filter> | |
1243 </data> | |
1244 </outputs> | |
1245 <tests> | |
1246 <test expect_num_outputs="1"> | |
1247 <param name="proteinassignedquantpepions" value="sample.quantAndProt"/> | |
1248 <param name="CorrelationLightHeavyThreshold" value="0.0"/> | |
1249 <conditional name="ModificationFilterCond"> | |
1250 <param name="ModificationFilter" value="All"/> | |
1251 </conditional> | |
1252 <section name="GlobalAggregationParams"> | |
1253 <section name="LabeledTransform"> | |
1254 <conditional name="LabeledTransformLightCond"> | |
1255 <param name="Type" value="None"/> | |
1256 </conditional> | |
1257 <conditional name="LabeledTransformHeavyCond"> | |
1258 <param name="Type" value="None"/> | |
1259 </conditional> | |
1260 <conditional name="LabeledTransformRatioCond"> | |
1261 <param name="Type" value="None"/> | |
1262 </conditional> | |
1263 </section> | |
1264 <section name="LabeledSingleFilters"> | |
1265 <section name="Light"> | |
1266 <param name="BiggerThan" value=""/> | |
1267 <param name="SmallerThan" value=""/> | |
1268 </section> | |
1269 <section name="Heavy"> | |
1270 <param name="BiggerThan" value=""/> | |
1271 <param name="SmallerThan" value=""/> | |
1272 </section> | |
1273 <section name="Ratio"> | |
1274 <param name="BiggerThan" value=""/> | |
1275 <param name="SmallerThan" value=""/> | |
1276 </section> | |
1277 </section> | |
1278 <section name="LabeledGroupFilters"> | |
1279 <section name="Light"> | |
1280 <param name="Tukey" value=""/> | |
1281 <param name="Stdev" value=""/> | |
1282 </section> | |
1283 <section name="Heavy"> | |
1284 <param name="Tukey" value=""/> | |
1285 <param name="Stdev" value=""/> | |
1286 </section> | |
1287 <section name="Ratio"> | |
1288 <param name="Tukey" value=""/> | |
1289 <param name="Stdev" value=""/> | |
1290 </section> | |
1291 </section> | |
1292 <section name="LabeledAggregation"> | |
1293 <param name="labeledAggregationLight" value="Mean"/> | |
1294 <param name="labeledAggregationHeavy" value="Mean"/> | |
1295 <param name="labeledAggregationRatio" value="Mean"/> | |
1296 </section> | |
1297 </section> | |
1298 <section name="AggregatePeptideChargeStatesParams"> | |
1299 <conditional name="AggregatePeptideChargeStatesParamsCond"> | |
1300 <param name="AggregateModifiedPeptidesParamsEnabled" value="no" /> | |
1301 </conditional> | |
1302 </section> | |
1303 <section name="AggregateModifiedPeptidesParams"> | |
1304 <conditional name="AggregateModifiedPeptidesParamsCond"> | |
1305 <param name="AggregateModifiedPeptidesParamsEnabled" value="no"/> | |
1306 </conditional> | |
1307 </section> | |
1308 <section name="AggregateToProteinGroupsParams"> | |
1309 <section name="LabeledTransform"> | |
1310 <conditional name="LabeledTransformLightCond"> | |
1311 <param name="Type" value="None"/> | |
1312 </conditional> | |
1313 <conditional name="LabeledTransformHeavyCond"> | |
1314 <param name="Type" value="None"/> | |
1315 </conditional> | |
1316 <conditional name="LabeledTransformRatioCond"> | |
1317 <param name="Type" value="None"/> | |
1318 </conditional> | |
1319 </section> | |
1320 <section name="LabeledSingleFilters"> | |
1321 <section name="Light"> | |
1322 <param name="BiggerThan" value=""/> | |
1323 <param name="SmallerThan" value=""/> | |
1324 </section> | |
1325 <section name="Heavy"> | |
1326 <param name="BiggerThan" value=""/> | |
1327 <param name="SmallerThan" value=""/> | |
1328 </section> | |
1329 <section name="Ratio"> | |
1330 <param name="BiggerThan" value=""/> | |
1331 <param name="SmallerThan" value=""/> | |
1332 </section> | |
1333 </section> | |
1334 <section name="LabeledGroupFilters"> | |
1335 <section name="Light"> | |
1336 <param name="Tukey" value=""/> | |
1337 <param name="Stdev" value=""/> | |
1338 </section> | |
1339 <section name="Heavy"> | |
1340 <param name="Tukey" value=""/> | |
1341 <param name="Stdev" value=""/> | |
1342 </section> | |
1343 <section name="Ratio"> | |
1344 <param name="Tukey" value=""/> | |
1345 <param name="Stdev" value=""/> | |
1346 </section> | |
1347 </section> | |
1348 <section name="LabeledAggregation"> | |
1349 <param name="labeledAggregationLight" value="Mean"/> | |
1350 <param name="labeledAggregationHeavy" value="Mean"/> | |
1351 <param name="labeledAggregationRatio" value="Mean"/> | |
1352 </section> | |
1353 </section> | |
1354 <param name="outputParamfile" value="false"/> | |
1355 </test> | |
1356 <test expect_num_outputs="2"> | |
1357 <param name="proteinassignedquantpepions" value="sample.quantAndProt"/> | |
1358 <param name="CorrelationLightHeavyThreshold" value="0.0"/> | |
1359 <conditional name="ModificationFilterCond"> | |
1360 <param name="ModificationFilter" value="All"/> | |
1361 </conditional> | |
1362 <section name="GlobalAggregationParams"> | |
1363 <section name="LabeledTransform"> | |
1364 <conditional name="LabeledTransformLightCond"> | |
1365 <param name="Type" value="None"/> | |
1366 </conditional> | |
1367 <conditional name="LabeledTransformHeavyCond"> | |
1368 <param name="Type" value="None"/> | |
1369 </conditional> | |
1370 <conditional name="LabeledTransformRatioCond"> | |
1371 <param name="Type" value="None"/> | |
1372 </conditional> | |
1373 </section> | |
1374 <section name="LabeledSingleFilters"> | |
1375 <section name="Light"> | |
1376 <param name="BiggerThan" value=""/> | |
1377 <param name="SmallerThan" value=""/> | |
1378 </section> | |
1379 <section name="Heavy"> | |
1380 <param name="BiggerThan" value=""/> | |
1381 <param name="SmallerThan" value=""/> | |
1382 </section> | |
1383 <section name="Ratio"> | |
1384 <param name="BiggerThan" value=""/> | |
1385 <param name="SmallerThan" value=""/> | |
1386 </section> | |
1387 </section> | |
1388 <section name="LabeledGroupFilters"> | |
1389 <section name="Light"> | |
1390 <param name="Tukey" value=""/> | |
1391 <param name="Stdev" value=""/> | |
1392 </section> | |
1393 <section name="Heavy"> | |
1394 <param name="Tukey" value=""/> | |
1395 <param name="Stdev" value=""/> | |
1396 </section> | |
1397 <section name="Ratio"> | |
1398 <param name="Tukey" value=""/> | |
1399 <param name="Stdev" value=""/> | |
1400 </section> | |
1401 </section> | |
1402 <section name="LabeledAggregation"> | |
1403 <param name="labeledAggregationLight" value="Mean"/> | |
1404 <param name="labeledAggregationHeavy" value="Mean"/> | |
1405 <param name="labeledAggregationRatio" value="Mean"/> | |
1406 </section> | |
1407 </section> | |
1408 <section name="AggregatePeptideChargeStatesParams"> | |
1409 <conditional name="AggregatePeptideChargeStatesParamsCond"> | |
1410 <param name="AggregateModifiedPeptidesParamsEnabled" value="no" /> | |
1411 </conditional> | |
1412 </section> | |
1413 <section name="AggregateModifiedPeptidesParams"> | |
1414 <conditional name="AggregateModifiedPeptidesParamsCond"> | |
1415 <param name="AggregateModifiedPeptidesParamsEnabled" value="no"/> | |
1416 </conditional> | |
1417 </section> | |
1418 <section name="AggregateToProteinGroupsParams"> | |
1419 <section name="LabeledTransform"> | |
1420 <conditional name="LabeledTransformLightCond"> | |
1421 <param name="Type" value="None"/> | |
1422 </conditional> | |
1423 <conditional name="LabeledTransformHeavyCond"> | |
1424 <param name="Type" value="None"/> | |
1425 </conditional> | |
1426 <conditional name="LabeledTransformRatioCond"> | |
1427 <param name="Type" value="None"/> | |
1428 </conditional> | |
1429 </section> | |
1430 <section name="LabeledSingleFilters"> | |
1431 <section name="Light"> | |
1432 <param name="BiggerThan" value=""/> | |
1433 <param name="SmallerThan" value=""/> | |
1434 </section> | |
1435 <section name="Heavy"> | |
1436 <param name="BiggerThan" value=""/> | |
1437 <param name="SmallerThan" value=""/> | |
1438 </section> | |
1439 <section name="Ratio"> | |
1440 <param name="BiggerThan" value=""/> | |
1441 <param name="SmallerThan" value=""/> | |
1442 </section> | |
1443 </section> | |
1444 <section name="LabeledGroupFilters"> | |
1445 <section name="Light"> | |
1446 <param name="Tukey" value=""/> | |
1447 <param name="Stdev" value=""/> | |
1448 </section> | |
1449 <section name="Heavy"> | |
1450 <param name="Tukey" value=""/> | |
1451 <param name="Stdev" value=""/> | |
1452 </section> | |
1453 <section name="Ratio"> | |
1454 <param name="Tukey" value=""/> | |
1455 <param name="Stdev" value=""/> | |
1456 </section> | |
1457 </section> | |
1458 <section name="LabeledAggregation"> | |
1459 <param name="labeledAggregationLight" value="Mean"/> | |
1460 <param name="labeledAggregationHeavy" value="Mean"/> | |
1461 <param name="labeledAggregationRatio" value="Mean"/> | |
1462 </section> | |
1463 </section> | |
1464 <param name="outputParamfile" value="true"/> | |
1465 <output name="out_paramfile" file="result_1.json"/> | |
1466 </test> | |
1467 <test expect_num_outputs="2"> | |
1468 <param name="proteinassignedquantpepions" value="sample.quantAndProt"/> | |
1469 <param name="CorrelationLightHeavyThreshold" value="1.0"/> | |
1470 <conditional name="ModificationFilterCond"> | |
1471 <param name="ModificationFilter" value="No"/> | |
1472 </conditional> | |
1473 <section name="GlobalAggregationParams"> | |
1474 <section name="LabeledTransform"> | |
1475 <conditional name="LabeledTransformLightCond"> | |
1476 <param name="Type" value="Log2"/> | |
1477 </conditional> | |
1478 <conditional name="LabeledTransformHeavyCond"> | |
1479 <param name="Type" value="Log2"/> | |
1480 </conditional> | |
1481 <conditional name="LabeledTransformRatioCond"> | |
1482 <param name="Type" value="Log2"/> | |
1483 </conditional> | |
1484 </section> | |
1485 <section name="LabeledSingleFilters"> | |
1486 <section name="Light"> | |
1487 <param name="BiggerThan" value="1"/> | |
1488 <param name="SmallerThan" value="2"/> | |
1489 </section> | |
1490 <section name="Heavy"> | |
1491 <param name="BiggerThan" value="1"/> | |
1492 <param name="SmallerThan" value="2"/> | |
1493 </section> | |
1494 <section name="Ratio"> | |
1495 <param name="BiggerThan" value="1"/> | |
1496 <param name="SmallerThan" value="2"/> | |
1497 </section> | |
1498 </section> | |
1499 <section name="LabeledGroupFilters"> | |
1500 <section name="Light"> | |
1501 <param name="Tukey" value="1"/> | |
1502 <param name="Stdev" value="2"/> | |
1503 </section> | |
1504 <section name="Heavy"> | |
1505 <param name="Tukey" value="1"/> | |
1506 <param name="Stdev" value="2"/> | |
1507 </section> | |
1508 <section name="Ratio"> | |
1509 <param name="Tukey" value="1"/> | |
1510 <param name="Stdev" value="2"/> | |
1511 </section> | |
1512 </section> | |
1513 <section name="LabeledAggregation"> | |
1514 <param name="labeledAggregationLight" value="Median"/> | |
1515 <param name="labeledAggregationHeavy" value="Sum"/> | |
1516 <param name="labeledAggregationRatio" value="Sum"/> | |
1517 </section> | |
1518 </section> | |
1519 <section name="AggregatePeptideChargeStatesParams"> | |
1520 <conditional name="AggregatePeptideChargeStatesParamsCond"> | |
1521 <param name="AggregatePeptideChargeStatesParamsEnabled" value="yes" /> | |
1522 <section name="LabeledTransform"> | |
1523 <conditional name="LabeledTransformLightCond"> | |
1524 <param name="Type" value="Log2"/> | |
1525 </conditional> | |
1526 <conditional name="LabeledTransformHeavyCond"> | |
1527 <param name="Type" value="Log2"/> | |
1528 </conditional> | |
1529 <conditional name="LabeledTransformRatioCond"> | |
1530 <param name="Type" value="Log2"/> | |
1531 </conditional> | |
1532 </section> | |
1533 <section name="LabeledSingleFilters"> | |
1534 <section name="Light"> | |
1535 <param name="BiggerThan" value="1"/> | |
1536 <param name="SmallerThan" value="2"/> | |
1537 </section> | |
1538 <section name="Heavy"> | |
1539 <param name="BiggerThan" value="1"/> | |
1540 <param name="SmallerThan" value="2"/> | |
1541 </section> | |
1542 <section name="Ratio"> | |
1543 <param name="BiggerThan" value="1"/> | |
1544 <param name="SmallerThan" value="2"/> | |
1545 </section> | |
1546 </section> | |
1547 <section name="LabeledGroupFilters"> | |
1548 <section name="Light"> | |
1549 <param name="Tukey" value="1"/> | |
1550 <param name="Stdev" value="2"/> | |
1551 </section> | |
1552 <section name="Heavy"> | |
1553 <param name="Tukey" value="1"/> | |
1554 <param name="Stdev" value="2"/> | |
1555 </section> | |
1556 <section name="Ratio"> | |
1557 <param name="Tukey" value="1"/> | |
1558 <param name="Stdev" value="2"/> | |
1559 </section> | |
1560 </section> | |
1561 <section name="LabeledAggregation"> | |
1562 <param name="labeledAggregationLight" value="Median"/> | |
1563 <param name="labeledAggregationHeavy" value="Sum"/> | |
1564 <param name="labeledAggregationRatio" value="Sum"/> | |
1565 </section> | |
1566 </conditional> | |
1567 </section> | |
1568 <section name="AggregateModifiedPeptidesParams"> | |
1569 <conditional name="AggregateModifiedPeptidesParamsCond"> | |
1570 <param name="AggregateModifiedPeptidesParamsEnabled" value="yes"/> | |
1571 <section name="LabeledTransform"> | |
1572 <conditional name="LabeledTransformLightCond"> | |
1573 <param name="Type" value="Log2"/> | |
1574 </conditional> | |
1575 <conditional name="LabeledTransformHeavyCond"> | |
1576 <param name="Type" value="Log2"/> | |
1577 </conditional> | |
1578 <conditional name="LabeledTransformRatioCond"> | |
1579 <param name="Type" value="Log2"/> | |
1580 </conditional> | |
1581 </section> | |
1582 <section name="LabeledSingleFilters"> | |
1583 <section name="Light"> | |
1584 <param name="BiggerThan" value="1"/> | |
1585 <param name="SmallerThan" value="2"/> | |
1586 </section> | |
1587 <section name="Heavy"> | |
1588 <param name="BiggerThan" value="1"/> | |
1589 <param name="SmallerThan" value="2"/> | |
1590 </section> | |
1591 <section name="Ratio"> | |
1592 <param name="BiggerThan" value="1"/> | |
1593 <param name="SmallerThan" value="2"/> | |
1594 </section> | |
1595 </section> | |
1596 <section name="LabeledGroupFilters"> | |
1597 <section name="Light"> | |
1598 <param name="Tukey" value="1"/> | |
1599 <param name="Stdev" value="2"/> | |
1600 </section> | |
1601 <section name="Heavy"> | |
1602 <param name="Tukey" value="1"/> | |
1603 <param name="Stdev" value="2"/> | |
1604 </section> | |
1605 <section name="Ratio"> | |
1606 <param name="Tukey" value="1"/> | |
1607 <param name="Stdev" value="2"/> | |
1608 </section> | |
1609 </section> | |
1610 <section name="LabeledAggregation"> | |
1611 <param name="labeledAggregationLight" value="Median"/> | |
1612 <param name="labeledAggregationHeavy" value="Sum"/> | |
1613 <param name="labeledAggregationRatio" value="Sum"/> | |
1614 </section> | |
1615 </conditional> | |
1616 </section> | |
1617 <section name="AggregateToProteinGroupsParams"> | |
1618 <section name="LabeledTransform"> | |
1619 <conditional name="LabeledTransformLightCond"> | |
1620 <param name="Type" value="Log2"/> | |
1621 </conditional> | |
1622 <conditional name="LabeledTransformHeavyCond"> | |
1623 <param name="Type" value="Log2"/> | |
1624 </conditional> | |
1625 <conditional name="LabeledTransformRatioCond"> | |
1626 <param name="Type" value="Log2"/> | |
1627 </conditional> | |
1628 </section> | |
1629 <section name="LabeledSingleFilters"> | |
1630 <section name="Light"> | |
1631 <param name="BiggerThan" value="1"/> | |
1632 <param name="SmallerThan" value="2"/> | |
1633 </section> | |
1634 <section name="Heavy"> | |
1635 <param name="BiggerThan" value="1"/> | |
1636 <param name="SmallerThan" value="2"/> | |
1637 </section> | |
1638 <section name="Ratio"> | |
1639 <param name="BiggerThan" value="1"/> | |
1640 <param name="SmallerThan" value="2"/> | |
1641 </section> | |
1642 </section> | |
1643 <section name="LabeledGroupFilters"> | |
1644 <section name="Light"> | |
1645 <param name="Tukey" value="1"/> | |
1646 <param name="Stdev" value="2"/> | |
1647 </section> | |
1648 <section name="Heavy"> | |
1649 <param name="Tukey" value="1"/> | |
1650 <param name="Stdev" value="2"/> | |
1651 </section> | |
1652 <section name="Ratio"> | |
1653 <param name="Tukey" value="1"/> | |
1654 <param name="Stdev" value="2"/> | |
1655 </section> | |
1656 </section> | |
1657 <section name="LabeledAggregation"> | |
1658 <param name="labeledAggregationLight" value="Median"/> | |
1659 <param name="labeledAggregationHeavy" value="Sum"/> | |
1660 <param name="labeledAggregationRatio" value="Sum"/> | |
1661 </section> | |
1662 </section> | |
1663 <param name="outputParamfile" value="true"/> | |
1664 <output name="out_paramfile" file="result_2.json"/> | |
1665 </test> | |
1666 <test expect_num_outputs="2"> | |
1667 <param name="proteinassignedquantpepions" value="sample.quantAndProt"/> | |
1668 <param name="CorrelationLightHeavyThreshold" value="1.0"/> | |
1669 <conditional name="ModificationFilterCond"> | |
1670 <param name="ModificationFilter" value="No"/> | |
1671 </conditional> | |
1672 <section name="GlobalAggregationParams"> | |
1673 <section name="LabeledTransform"> | |
1674 <conditional name="LabeledTransformLightCond"> | |
1675 <param name="Type" value="Substract"/> | |
1676 <param name="Value" value="2"/> | |
1677 </conditional> | |
1678 <conditional name="LabeledTransformHeavyCond"> | |
1679 <param name="Type" value="Add"/> | |
1680 <param name="Value" value="3"/> | |
1681 </conditional> | |
1682 <conditional name="LabeledTransformRatioCond"> | |
1683 <param name="Type" value="DivideBy"/> | |
1684 <param name="Value" value="4"/> | |
1685 </conditional> | |
1686 </section> | |
1687 <section name="LabeledSingleFilters"> | |
1688 <section name="Light"> | |
1689 <param name="BiggerThan" value="1"/> | |
1690 <param name="SmallerThan" value="2"/> | |
1691 </section> | |
1692 <section name="Heavy"> | |
1693 <param name="BiggerThan" value="1"/> | |
1694 <param name="SmallerThan" value="2"/> | |
1695 </section> | |
1696 <section name="Ratio"> | |
1697 <param name="BiggerThan" value="1"/> | |
1698 <param name="SmallerThan" value="2"/> | |
1699 </section> | |
1700 </section> | |
1701 <section name="LabeledGroupFilters"> | |
1702 <section name="Light"> | |
1703 <param name="Tukey" value="1"/> | |
1704 <param name="Stdev" value="2"/> | |
1705 </section> | |
1706 <section name="Heavy"> | |
1707 <param name="Tukey" value="1"/> | |
1708 <param name="Stdev" value="2"/> | |
1709 </section> | |
1710 <section name="Ratio"> | |
1711 <param name="Tukey" value="1"/> | |
1712 <param name="Stdev" value="2"/> | |
1713 </section> | |
1714 </section> | |
1715 <section name="LabeledAggregation"> | |
1716 <param name="labeledAggregationLight" value="Median"/> | |
1717 <param name="labeledAggregationHeavy" value="Sum"/> | |
1718 <param name="labeledAggregationRatio" value="Sum"/> | |
1719 </section> | |
1720 </section> | |
1721 <section name="AggregatePeptideChargeStatesParams"> | |
1722 <conditional name="AggregatePeptideChargeStatesParamsCond"> | |
1723 <param name="AggregatePeptideChargeStatesParamsEnabled" value="yes" /> | |
1724 <section name="LabeledTransform"> | |
1725 <conditional name="LabeledTransformLightCond"> | |
1726 <param name="Type" value="Log2"/> | |
1727 </conditional> | |
1728 <conditional name="LabeledTransformHeavyCond"> | |
1729 <param name="Type" value="Log2"/> | |
1730 </conditional> | |
1731 <conditional name="LabeledTransformRatioCond"> | |
1732 <param name="Type" value="Log2"/> | |
1733 </conditional> | |
1734 </section> | |
1735 <section name="LabeledSingleFilters"> | |
1736 <section name="Light"> | |
1737 <param name="BiggerThan" value="1"/> | |
1738 <param name="SmallerThan" value="2"/> | |
1739 </section> | |
1740 <section name="Heavy"> | |
1741 <param name="BiggerThan" value="1"/> | |
1742 <param name="SmallerThan" value="2"/> | |
1743 </section> | |
1744 <section name="Ratio"> | |
1745 <param name="BiggerThan" value="1"/> | |
1746 <param name="SmallerThan" value="2"/> | |
1747 </section> | |
1748 </section> | |
1749 <section name="LabeledGroupFilters"> | |
1750 <section name="Light"> | |
1751 <param name="Tukey" value="1"/> | |
1752 <param name="Stdev" value="2"/> | |
1753 </section> | |
1754 <section name="Heavy"> | |
1755 <param name="Tukey" value="1"/> | |
1756 <param name="Stdev" value="2"/> | |
1757 </section> | |
1758 <section name="Ratio"> | |
1759 <param name="Tukey" value="1"/> | |
1760 <param name="Stdev" value="2"/> | |
1761 </section> | |
1762 </section> | |
1763 <section name="LabeledAggregation"> | |
1764 <param name="labeledAggregationLight" value="Median"/> | |
1765 <param name="labeledAggregationHeavy" value="Sum"/> | |
1766 <param name="labeledAggregationRatio" value="Sum"/> | |
1767 </section> | |
1768 </conditional> | |
1769 </section> | |
1770 <section name="AggregateModifiedPeptidesParams"> | |
1771 <conditional name="AggregateModifiedPeptidesParamsCond"> | |
1772 <param name="AggregateModifiedPeptidesParamsEnabled" value="yes"/> | |
1773 <section name="LabeledTransform"> | |
1774 <conditional name="LabeledTransformLightCond"> | |
1775 <param name="Type" value="Log2"/> | |
1776 </conditional> | |
1777 <conditional name="LabeledTransformHeavyCond"> | |
1778 <param name="Type" value="Log2"/> | |
1779 </conditional> | |
1780 <conditional name="LabeledTransformRatioCond"> | |
1781 <param name="Type" value="Log2"/> | |
1782 </conditional> | |
1783 </section> | |
1784 <section name="LabeledSingleFilters"> | |
1785 <section name="Light"> | |
1786 <param name="BiggerThan" value="1"/> | |
1787 <param name="SmallerThan" value="2"/> | |
1788 </section> | |
1789 <section name="Heavy"> | |
1790 <param name="BiggerThan" value="1"/> | |
1791 <param name="SmallerThan" value="2"/> | |
1792 </section> | |
1793 <section name="Ratio"> | |
1794 <param name="BiggerThan" value="1"/> | |
1795 <param name="SmallerThan" value="2"/> | |
1796 </section> | |
1797 </section> | |
1798 <section name="LabeledGroupFilters"> | |
1799 <section name="Light"> | |
1800 <param name="Tukey" value="1"/> | |
1801 <param name="Stdev" value="2"/> | |
1802 </section> | |
1803 <section name="Heavy"> | |
1804 <param name="Tukey" value="1"/> | |
1805 <param name="Stdev" value="2"/> | |
1806 </section> | |
1807 <section name="Ratio"> | |
1808 <param name="Tukey" value="1"/> | |
1809 <param name="Stdev" value="2"/> | |
1810 </section> | |
1811 </section> | |
1812 <section name="LabeledAggregation"> | |
1813 <param name="labeledAggregationLight" value="Median"/> | |
1814 <param name="labeledAggregationHeavy" value="Sum"/> | |
1815 <param name="labeledAggregationRatio" value="Sum"/> | |
1816 </section> | |
1817 </conditional> | |
1818 </section> | |
1819 <section name="AggregateToProteinGroupsParams"> | |
1820 <section name="LabeledTransform"> | |
1821 <conditional name="LabeledTransformLightCond"> | |
1822 <param name="Type" value="Log2"/> | |
1823 </conditional> | |
1824 <conditional name="LabeledTransformHeavyCond"> | |
1825 <param name="Type" value="Log2"/> | |
1826 </conditional> | |
1827 <conditional name="LabeledTransformRatioCond"> | |
1828 <param name="Type" value="Log2"/> | |
1829 </conditional> | |
1830 </section> | |
1831 <section name="LabeledSingleFilters"> | |
1832 <section name="Light"> | |
1833 <param name="BiggerThan" value="1"/> | |
1834 <param name="SmallerThan" value="2"/> | |
1835 </section> | |
1836 <section name="Heavy"> | |
1837 <param name="BiggerThan" value="1"/> | |
1838 <param name="SmallerThan" value=""/> | |
1839 </section> | |
1840 <section name="Ratio"> | |
1841 <param name="BiggerThan" value=""/> | |
1842 <param name="SmallerThan" value=""/> | |
1843 </section> | |
1844 </section> | |
1845 <section name="LabeledGroupFilters"> | |
1846 <section name="Light"> | |
1847 <param name="Tukey" value="1"/> | |
1848 <param name="Stdev" value="2"/> | |
1849 </section> | |
1850 <section name="Heavy"> | |
1851 <param name="Tukey" value=""/> | |
1852 <param name="Stdev" value="2"/> | |
1853 </section> | |
1854 <section name="Ratio"> | |
1855 <param name="Tukey" value=""/> | |
1856 <param name="Stdev" value=""/> | |
1857 </section> | |
1858 </section> | |
1859 <section name="LabeledAggregation"> | |
1860 <param name="labeledAggregationLight" value="Median"/> | |
1861 <param name="labeledAggregationHeavy" value="Sum"/> | |
1862 <param name="labeledAggregationRatio" value="Sum"/> | |
1863 </section> | |
1864 </section> | |
1865 <param name="outputParamfile" value="true"/> | |
1866 <output name="out_paramfile" file="result_3.json"/> | |
1867 </test> | |
1868 <test expect_num_outputs="2"> | |
1869 <param name="proteinassignedquantpepions" value="sample.quantAndProt"/> | |
1870 <param name="CorrelationLightHeavyThreshold" value="1.0"/> | |
1871 <conditional name="ModificationFilterCond"> | |
1872 <param name="ModificationFilter" value="No"/> | |
1873 </conditional> | |
1874 <section name="GlobalAggregationParams"> | |
1875 <section name="LabeledTransform"> | |
1876 <conditional name="LabeledTransformLightCond"> | |
1877 <param name="Type" value="Substract"/> | |
1878 <param name="Value" value="2"/> | |
1879 </conditional> | |
1880 <conditional name="LabeledTransformHeavyCond"> | |
1881 <param name="Type" value="Add"/> | |
1882 <param name="Value" value="3"/> | |
1883 </conditional> | |
1884 <conditional name="LabeledTransformRatioCond"> | |
1885 <param name="Type" value="DivideBy"/> | |
1886 <param name="Value" value="4"/> | |
1887 </conditional> | |
1888 </section> | |
1889 <section name="LabeledSingleFilters"> | |
1890 <section name="Light"> | |
1891 <param name="BiggerThan" value="1"/> | |
1892 <param name="SmallerThan" value="2"/> | |
1893 </section> | |
1894 <section name="Heavy"> | |
1895 <param name="BiggerThan" value="1"/> | |
1896 <param name="SmallerThan" value="2"/> | |
1897 </section> | |
1898 <section name="Ratio"> | |
1899 <param name="BiggerThan" value="1"/> | |
1900 <param name="SmallerThan" value="2"/> | |
1901 </section> | |
1902 </section> | |
1903 <section name="LabeledGroupFilters"> | |
1904 <section name="Light"> | |
1905 <param name="Tukey" value="1"/> | |
1906 <param name="Stdev" value="2"/> | |
1907 </section> | |
1908 <section name="Heavy"> | |
1909 <param name="Tukey" value="1"/> | |
1910 <param name="Stdev" value="2"/> | |
1911 </section> | |
1912 <section name="Ratio"> | |
1913 <param name="Tukey" value="1"/> | |
1914 <param name="Stdev" value="2"/> | |
1915 </section> | |
1916 </section> | |
1917 <section name="LabeledAggregation"> | |
1918 <param name="labeledAggregationLight" value="Median"/> | |
1919 <param name="labeledAggregationHeavy" value="Sum"/> | |
1920 <param name="labeledAggregationRatio" value="Sum"/> | |
1921 </section> | |
1922 </section> | |
1923 <section name="AggregatePeptideChargeStatesParams"> | |
1924 <conditional name="AggregatePeptideChargeStatesParamsCond"> | |
1925 <param name="AggregatePeptideChargeStatesParamsEnabled" value="yes" /> | |
1926 <section name="LabeledTransform"> | |
1927 <conditional name="LabeledTransformLightCond"> | |
1928 <param name="Type" value="Substract"/> | |
1929 <param name="Value" value="2"/> | |
1930 </conditional> | |
1931 <conditional name="LabeledTransformHeavyCond"> | |
1932 <param name="Type" value="Add"/> | |
1933 <param name="Value" value="3"/> | |
1934 </conditional> | |
1935 <conditional name="LabeledTransformRatioCond"> | |
1936 <param name="Type" value="DivideBy"/> | |
1937 <param name="Value" value="4"/> | |
1938 </conditional> | |
1939 </section> | |
1940 <section name="LabeledSingleFilters"> | |
1941 <section name="Light"> | |
1942 <param name="BiggerThan" value="1"/> | |
1943 <param name="SmallerThan" value="2"/> | |
1944 </section> | |
1945 <section name="Heavy"> | |
1946 <param name="BiggerThan" value="1"/> | |
1947 <param name="SmallerThan" value="2"/> | |
1948 </section> | |
1949 <section name="Ratio"> | |
1950 <param name="BiggerThan" value="1"/> | |
1951 <param name="SmallerThan" value="2"/> | |
1952 </section> | |
1953 </section> | |
1954 <section name="LabeledGroupFilters"> | |
1955 <section name="Light"> | |
1956 <param name="Tukey" value="1"/> | |
1957 <param name="Stdev" value="2"/> | |
1958 </section> | |
1959 <section name="Heavy"> | |
1960 <param name="Tukey" value="1"/> | |
1961 <param name="Stdev" value="2"/> | |
1962 </section> | |
1963 <section name="Ratio"> | |
1964 <param name="Tukey" value="1"/> | |
1965 <param name="Stdev" value="2"/> | |
1966 </section> | |
1967 </section> | |
1968 <section name="LabeledAggregation"> | |
1969 <param name="labeledAggregationLight" value="Median"/> | |
1970 <param name="labeledAggregationHeavy" value="Sum"/> | |
1971 <param name="labeledAggregationRatio" value="Sum"/> | |
1972 </section> | |
1973 </conditional> | |
1974 </section> | |
1975 <section name="AggregateModifiedPeptidesParams"> | |
1976 <conditional name="AggregateModifiedPeptidesParamsCond"> | |
1977 <param name="AggregateModifiedPeptidesParamsEnabled" value="yes"/> | |
1978 <section name="LabeledTransform"> | |
1979 <conditional name="LabeledTransformLightCond"> | |
1980 <param name="Type" value="Substract"/> | |
1981 <param name="Value" value="2"/> | |
1982 </conditional> | |
1983 <conditional name="LabeledTransformHeavyCond"> | |
1984 <param name="Type" value="Add"/> | |
1985 <param name="Value" value="3"/> | |
1986 </conditional> | |
1987 <conditional name="LabeledTransformRatioCond"> | |
1988 <param name="Type" value="DivideBy"/> | |
1989 <param name="Value" value="4"/> | |
1990 </conditional> | |
1991 </section> | |
1992 <section name="LabeledSingleFilters"> | |
1993 <section name="Light"> | |
1994 <param name="BiggerThan" value="1"/> | |
1995 <param name="SmallerThan" value="2"/> | |
1996 </section> | |
1997 <section name="Heavy"> | |
1998 <param name="BiggerThan" value="1"/> | |
1999 <param name="SmallerThan" value="2"/> | |
2000 </section> | |
2001 <section name="Ratio"> | |
2002 <param name="BiggerThan" value="1"/> | |
2003 <param name="SmallerThan" value="2"/> | |
2004 </section> | |
2005 </section> | |
2006 <section name="LabeledGroupFilters"> | |
2007 <section name="Light"> | |
2008 <param name="Tukey" value="1"/> | |
2009 <param name="Stdev" value="2"/> | |
2010 </section> | |
2011 <section name="Heavy"> | |
2012 <param name="Tukey" value="1"/> | |
2013 <param name="Stdev" value="2"/> | |
2014 </section> | |
2015 <section name="Ratio"> | |
2016 <param name="Tukey" value="1"/> | |
2017 <param name="Stdev" value="2"/> | |
2018 </section> | |
2019 </section> | |
2020 <section name="LabeledAggregation"> | |
2021 <param name="labeledAggregationLight" value="Median"/> | |
2022 <param name="labeledAggregationHeavy" value="Sum"/> | |
2023 <param name="labeledAggregationRatio" value="Sum"/> | |
2024 </section> | |
2025 </conditional> | |
2026 </section> | |
2027 <section name="AggregateToProteinGroupsParams"> | |
2028 <section name="LabeledTransform"> | |
2029 <conditional name="LabeledTransformLightCond"> | |
2030 <param name="Type" value="Substract"/> | |
2031 <param name="Value" value="2"/> | |
2032 </conditional> | |
2033 <conditional name="LabeledTransformHeavyCond"> | |
2034 <param name="Type" value="Add"/> | |
2035 <param name="Value" value="3"/> | |
2036 </conditional> | |
2037 <conditional name="LabeledTransformRatioCond"> | |
2038 <param name="Type" value="DivideBy"/> | |
2039 <param name="Value" value="4"/> | |
2040 </conditional> | |
2041 </section> | |
2042 <section name="LabeledSingleFilters"> | |
2043 <section name="Light"> | |
2044 <param name="BiggerThan" value="1"/> | |
2045 <param name="SmallerThan" value="2"/> | |
2046 </section> | |
2047 <section name="Heavy"> | |
2048 <param name="BiggerThan" value="1"/> | |
2049 <param name="SmallerThan" value=""/> | |
2050 </section> | |
2051 <section name="Ratio"> | |
2052 <param name="BiggerThan" value=""/> | |
2053 <param name="SmallerThan" value=""/> | |
2054 </section> | |
2055 </section> | |
2056 <section name="LabeledGroupFilters"> | |
2057 <section name="Light"> | |
2058 <param name="Tukey" value="1"/> | |
2059 <param name="Stdev" value="2"/> | |
2060 </section> | |
2061 <section name="Heavy"> | |
2062 <param name="Tukey" value=""/> | |
2063 <param name="Stdev" value="2"/> | |
2064 </section> | |
2065 <section name="Ratio"> | |
2066 <param name="Tukey" value=""/> | |
2067 <param name="Stdev" value=""/> | |
2068 </section> | |
2069 </section> | |
2070 <section name="LabeledAggregation"> | |
2071 <param name="labeledAggregationLight" value="Median"/> | |
2072 <param name="labeledAggregationHeavy" value="Sum"/> | |
2073 <param name="labeledAggregationRatio" value="Sum"/> | |
2074 </section> | |
2075 </section> | |
2076 <param name="outputParamfile" value="true"/> | |
2077 <output name="out_paramfile" file="result_4.json"/> | |
2078 </test> | |
2079 <test expect_num_outputs="2"> | |
2080 <param name="proteinassignedquantpepions" value="sample.quantAndProt"/> | |
2081 <param name="CorrelationLightHeavyThreshold" value="1.0"/> | |
2082 <conditional name="ModificationFilterCond"> | |
2083 <param name="ModificationFilter" value="No"/> | |
2084 </conditional> | |
2085 <section name="GlobalAggregationParams"> | |
2086 <section name="LabeledTransform"> | |
2087 <conditional name="LabeledTransformLightCond"> | |
2088 <param name="Type" value="Substract"/> | |
2089 <param name="Value" value="2"/> | |
2090 </conditional> | |
2091 <conditional name="LabeledTransformHeavyCond"> | |
2092 <param name="Type" value="Add"/> | |
2093 <param name="Value" value="3"/> | |
2094 </conditional> | |
2095 <conditional name="LabeledTransformRatioCond"> | |
2096 <param name="Type" value="DivideBy"/> | |
2097 <param name="Value" value="4"/> | |
2098 </conditional> | |
2099 </section> | |
2100 <section name="LabeledSingleFilters"> | |
2101 <section name="Light"> | |
2102 <param name="BiggerThan" value="1"/> | |
2103 <param name="SmallerThan" value="2"/> | |
2104 </section> | |
2105 <section name="Heavy"> | |
2106 <param name="BiggerThan" value="1"/> | |
2107 <param name="SmallerThan" value="2"/> | |
2108 </section> | |
2109 <section name="Ratio"> | |
2110 <param name="BiggerThan" value="1"/> | |
2111 <param name="SmallerThan" value="2"/> | |
2112 </section> | |
2113 </section> | |
2114 <section name="LabeledGroupFilters"> | |
2115 <section name="Light"> | |
2116 <param name="Tukey" value="1"/> | |
2117 <param name="Stdev" value="2"/> | |
2118 </section> | |
2119 <section name="Heavy"> | |
2120 <param name="Tukey" value="1"/> | |
2121 <param name="Stdev" value="2"/> | |
2122 </section> | |
2123 <section name="Ratio"> | |
2124 <param name="Tukey" value="1"/> | |
2125 <param name="Stdev" value="2"/> | |
2126 </section> | |
2127 </section> | |
2128 <section name="LabeledAggregation"> | |
2129 <param name="labeledAggregationLight" value="Sum"/> | |
2130 <param name="labeledAggregationHeavy" value="Median"/> | |
2131 <param name="labeledAggregationRatio" value="Median"/> | |
2132 </section> | |
2133 </section> | |
2134 <section name="AggregatePeptideChargeStatesParams"> | |
2135 <conditional name="AggregatePeptideChargeStatesParamsCond"> | |
2136 <param name="AggregatePeptideChargeStatesParamsEnabled" value="yes" /> | |
2137 <section name="LabeledTransform"> | |
2138 <conditional name="LabeledTransformLightCond"> | |
2139 <param name="Type" value="Substract"/> | |
2140 <param name="Value" value="2"/> | |
2141 </conditional> | |
2142 <conditional name="LabeledTransformHeavyCond"> | |
2143 <param name="Type" value="Add"/> | |
2144 <param name="Value" value="3"/> | |
2145 </conditional> | |
2146 <conditional name="LabeledTransformRatioCond"> | |
2147 <param name="Type" value="DivideBy"/> | |
2148 <param name="Value" value="4"/> | |
2149 </conditional> | |
2150 </section> | |
2151 <section name="LabeledSingleFilters"> | |
2152 <section name="Light"> | |
2153 <param name="BiggerThan" value="1"/> | |
2154 <param name="SmallerThan" value="2"/> | |
2155 </section> | |
2156 <section name="Heavy"> | |
2157 <param name="BiggerThan" value="1"/> | |
2158 <param name="SmallerThan" value="2"/> | |
2159 </section> | |
2160 <section name="Ratio"> | |
2161 <param name="BiggerThan" value="1"/> | |
2162 <param name="SmallerThan" value="2"/> | |
2163 </section> | |
2164 </section> | |
2165 <section name="LabeledGroupFilters"> | |
2166 <section name="Light"> | |
2167 <param name="Tukey" value="1"/> | |
2168 <param name="Stdev" value="2"/> | |
2169 </section> | |
2170 <section name="Heavy"> | |
2171 <param name="Tukey" value="1"/> | |
2172 <param name="Stdev" value="2"/> | |
2173 </section> | |
2174 <section name="Ratio"> | |
2175 <param name="Tukey" value="1"/> | |
2176 <param name="Stdev" value="2"/> | |
2177 </section> | |
2178 </section> | |
2179 <section name="LabeledAggregation"> | |
2180 <param name="labeledAggregationLight" value="Sum"/> | |
2181 <param name="labeledAggregationHeavy" value="Median"/> | |
2182 <param name="labeledAggregationRatio" value="Median"/> | |
2183 </section> | |
2184 </conditional> | |
2185 </section> | |
2186 <section name="AggregateModifiedPeptidesParams"> | |
2187 <conditional name="AggregateModifiedPeptidesParamsCond"> | |
2188 <param name="AggregateModifiedPeptidesParamsEnabled" value="yes"/> | |
2189 <section name="LabeledTransform"> | |
2190 <conditional name="LabeledTransformLightCond"> | |
2191 <param name="Type" value="Substract"/> | |
2192 <param name="Value" value="2"/> | |
2193 </conditional> | |
2194 <conditional name="LabeledTransformHeavyCond"> | |
2195 <param name="Type" value="Add"/> | |
2196 <param name="Value" value="3"/> | |
2197 </conditional> | |
2198 <conditional name="LabeledTransformRatioCond"> | |
2199 <param name="Type" value="DivideBy"/> | |
2200 <param name="Value" value="4"/> | |
2201 </conditional> | |
2202 </section> | |
2203 <section name="LabeledSingleFilters"> | |
2204 <section name="Light"> | |
2205 <param name="BiggerThan" value="1"/> | |
2206 <param name="SmallerThan" value="2"/> | |
2207 </section> | |
2208 <section name="Heavy"> | |
2209 <param name="BiggerThan" value="1"/> | |
2210 <param name="SmallerThan" value="2"/> | |
2211 </section> | |
2212 <section name="Ratio"> | |
2213 <param name="BiggerThan" value="1"/> | |
2214 <param name="SmallerThan" value="2"/> | |
2215 </section> | |
2216 </section> | |
2217 <section name="LabeledGroupFilters"> | |
2218 <section name="Light"> | |
2219 <param name="Tukey" value="1"/> | |
2220 <param name="Stdev" value="2"/> | |
2221 </section> | |
2222 <section name="Heavy"> | |
2223 <param name="Tukey" value="1"/> | |
2224 <param name="Stdev" value="2"/> | |
2225 </section> | |
2226 <section name="Ratio"> | |
2227 <param name="Tukey" value="1"/> | |
2228 <param name="Stdev" value="2"/> | |
2229 </section> | |
2230 </section> | |
2231 <section name="LabeledAggregation"> | |
2232 <param name="labeledAggregationLight" value="Sum"/> | |
2233 <param name="labeledAggregationHeavy" value="Median"/> | |
2234 <param name="labeledAggregationRatio" value="Median"/> | |
2235 </section> | |
2236 </conditional> | |
2237 </section> | |
2238 <section name="AggregateToProteinGroupsParams"> | |
2239 <section name="LabeledTransform"> | |
2240 <conditional name="LabeledTransformLightCond"> | |
2241 <param name="Type" value="Substract"/> | |
2242 <param name="Value" value="2"/> | |
2243 </conditional> | |
2244 <conditional name="LabeledTransformHeavyCond"> | |
2245 <param name="Type" value="Add"/> | |
2246 <param name="Value" value="3"/> | |
2247 </conditional> | |
2248 <conditional name="LabeledTransformRatioCond"> | |
2249 <param name="Type" value="DivideBy"/> | |
2250 <param name="Value" value="4"/> | |
2251 </conditional> | |
2252 </section> | |
2253 <section name="LabeledSingleFilters"> | |
2254 <section name="Light"> | |
2255 <param name="BiggerThan" value="1"/> | |
2256 <param name="SmallerThan" value="2"/> | |
2257 </section> | |
2258 <section name="Heavy"> | |
2259 <param name="BiggerThan" value="1"/> | |
2260 <param name="SmallerThan" value=""/> | |
2261 </section> | |
2262 <section name="Ratio"> | |
2263 <param name="BiggerThan" value=""/> | |
2264 <param name="SmallerThan" value=""/> | |
2265 </section> | |
2266 </section> | |
2267 <section name="LabeledGroupFilters"> | |
2268 <section name="Light"> | |
2269 <param name="Tukey" value="1"/> | |
2270 <param name="Stdev" value="2"/> | |
2271 </section> | |
2272 <section name="Heavy"> | |
2273 <param name="Tukey" value=""/> | |
2274 <param name="Stdev" value="2"/> | |
2275 </section> | |
2276 <section name="Ratio"> | |
2277 <param name="Tukey" value=""/> | |
2278 <param name="Stdev" value=""/> | |
2279 </section> | |
2280 </section> | |
2281 <section name="LabeledAggregation"> | |
2282 <param name="labeledAggregationLight" value="Sum"/> | |
2283 <param name="labeledAggregationHeavy" value="Median"/> | |
2284 <param name="labeledAggregationRatio" value="Median"/> | |
2285 </section> | |
2286 </section> | |
2287 <param name="outputParamfile" value="true"/> | |
2288 <output name="out_paramfile" file="result_5.json"/> | |
2289 </test> | |
2290 <test expect_num_outputs="2"> | |
2291 <param name="proteinassignedquantpepions" value="sample.quantAndProt"/> | |
2292 <param name="CorrelationLightHeavyThreshold" value="1.0"/> | |
2293 <conditional name="ModificationFilterCond"> | |
2294 <param name="ModificationFilter" value="UseOnly"/> | |
2295 <param name="ModificationFilterSequence" value="Acetylation'ProtNTerm',Carbamidomethyl'Cys',Oxidation'Met',Phosphorylation'Ser'Thr'Tyr',Pyro_Glu'GluNterm',Pyro_Glu'GlnNterm'"/> | |
2296 </conditional> | |
2297 <section name="GlobalAggregationParams"> | |
2298 <section name="LabeledTransform"> | |
2299 <conditional name="LabeledTransformLightCond"> | |
2300 <param name="Type" value="Substract"/> | |
2301 <param name="Value" value="2"/> | |
2302 </conditional> | |
2303 <conditional name="LabeledTransformHeavyCond"> | |
2304 <param name="Type" value="Add"/> | |
2305 <param name="Value" value="3"/> | |
2306 </conditional> | |
2307 <conditional name="LabeledTransformRatioCond"> | |
2308 <param name="Type" value="DivideBy"/> | |
2309 <param name="Value" value="4"/> | |
2310 </conditional> | |
2311 </section> | |
2312 <section name="LabeledSingleFilters"> | |
2313 <section name="Light"> | |
2314 <param name="BiggerThan" value="1"/> | |
2315 <param name="SmallerThan" value="2"/> | |
2316 </section> | |
2317 <section name="Heavy"> | |
2318 <param name="BiggerThan" value="1"/> | |
2319 <param name="SmallerThan" value="2"/> | |
2320 </section> | |
2321 <section name="Ratio"> | |
2322 <param name="BiggerThan" value="1"/> | |
2323 <param name="SmallerThan" value="2"/> | |
2324 </section> | |
2325 </section> | |
2326 <section name="LabeledGroupFilters"> | |
2327 <section name="Light"> | |
2328 <param name="Tukey" value="1"/> | |
2329 <param name="Stdev" value="2"/> | |
2330 </section> | |
2331 <section name="Heavy"> | |
2332 <param name="Tukey" value="1"/> | |
2333 <param name="Stdev" value="2"/> | |
2334 </section> | |
2335 <section name="Ratio"> | |
2336 <param name="Tukey" value="1"/> | |
2337 <param name="Stdev" value="2"/> | |
2338 </section> | |
2339 </section> | |
2340 <section name="LabeledAggregation"> | |
2341 <param name="labeledAggregationLight" value="Sum"/> | |
2342 <param name="labeledAggregationHeavy" value="Median"/> | |
2343 <param name="labeledAggregationRatio" value="Median"/> | |
2344 </section> | |
2345 </section> | |
2346 <section name="AggregatePeptideChargeStatesParams"> | |
2347 <conditional name="AggregatePeptideChargeStatesParamsCond"> | |
2348 <param name="AggregatePeptideChargeStatesParamsEnabled" value="yes" /> | |
2349 <section name="LabeledTransform"> | |
2350 <conditional name="LabeledTransformLightCond"> | |
2351 <param name="Type" value="Substract"/> | |
2352 <param name="Value" value="2"/> | |
2353 </conditional> | |
2354 <conditional name="LabeledTransformHeavyCond"> | |
2355 <param name="Type" value="Add"/> | |
2356 <param name="Value" value="3"/> | |
2357 </conditional> | |
2358 <conditional name="LabeledTransformRatioCond"> | |
2359 <param name="Type" value="DivideBy"/> | |
2360 <param name="Value" value="4"/> | |
2361 </conditional> | |
2362 </section> | |
2363 <section name="LabeledSingleFilters"> | |
2364 <section name="Light"> | |
2365 <param name="BiggerThan" value="1"/> | |
2366 <param name="SmallerThan" value="2"/> | |
2367 </section> | |
2368 <section name="Heavy"> | |
2369 <param name="BiggerThan" value="1"/> | |
2370 <param name="SmallerThan" value="2"/> | |
2371 </section> | |
2372 <section name="Ratio"> | |
2373 <param name="BiggerThan" value="1"/> | |
2374 <param name="SmallerThan" value="2"/> | |
2375 </section> | |
2376 </section> | |
2377 <section name="LabeledGroupFilters"> | |
2378 <section name="Light"> | |
2379 <param name="Tukey" value="1"/> | |
2380 <param name="Stdev" value="2"/> | |
2381 </section> | |
2382 <section name="Heavy"> | |
2383 <param name="Tukey" value="1"/> | |
2384 <param name="Stdev" value="2"/> | |
2385 </section> | |
2386 <section name="Ratio"> | |
2387 <param name="Tukey" value="1"/> | |
2388 <param name="Stdev" value="2"/> | |
2389 </section> | |
2390 </section> | |
2391 <section name="LabeledAggregation"> | |
2392 <param name="labeledAggregationLight" value="Sum"/> | |
2393 <param name="labeledAggregationHeavy" value="Median"/> | |
2394 <param name="labeledAggregationRatio" value="Median"/> | |
2395 </section> | |
2396 </conditional> | |
2397 </section> | |
2398 <section name="AggregateModifiedPeptidesParams"> | |
2399 <conditional name="AggregateModifiedPeptidesParamsCond"> | |
2400 <param name="AggregateModifiedPeptidesParamsEnabled" value="yes"/> | |
2401 <section name="LabeledTransform"> | |
2402 <conditional name="LabeledTransformLightCond"> | |
2403 <param name="Type" value="Substract"/> | |
2404 <param name="Value" value="2"/> | |
2405 </conditional> | |
2406 <conditional name="LabeledTransformHeavyCond"> | |
2407 <param name="Type" value="Add"/> | |
2408 <param name="Value" value="3"/> | |
2409 </conditional> | |
2410 <conditional name="LabeledTransformRatioCond"> | |
2411 <param name="Type" value="DivideBy"/> | |
2412 <param name="Value" value="4"/> | |
2413 </conditional> | |
2414 </section> | |
2415 <section name="LabeledSingleFilters"> | |
2416 <section name="Light"> | |
2417 <param name="BiggerThan" value="1"/> | |
2418 <param name="SmallerThan" value="2"/> | |
2419 </section> | |
2420 <section name="Heavy"> | |
2421 <param name="BiggerThan" value="1"/> | |
2422 <param name="SmallerThan" value="2"/> | |
2423 </section> | |
2424 <section name="Ratio"> | |
2425 <param name="BiggerThan" value="1"/> | |
2426 <param name="SmallerThan" value="2"/> | |
2427 </section> | |
2428 </section> | |
2429 <section name="LabeledGroupFilters"> | |
2430 <section name="Light"> | |
2431 <param name="Tukey" value="1"/> | |
2432 <param name="Stdev" value="2"/> | |
2433 </section> | |
2434 <section name="Heavy"> | |
2435 <param name="Tukey" value="1"/> | |
2436 <param name="Stdev" value="2"/> | |
2437 </section> | |
2438 <section name="Ratio"> | |
2439 <param name="Tukey" value="1"/> | |
2440 <param name="Stdev" value="2"/> | |
2441 </section> | |
2442 </section> | |
2443 <section name="LabeledAggregation"> | |
2444 <param name="labeledAggregationLight" value="Sum"/> | |
2445 <param name="labeledAggregationHeavy" value="Median"/> | |
2446 <param name="labeledAggregationRatio" value="Median"/> | |
2447 </section> | |
2448 </conditional> | |
2449 </section> | |
2450 <section name="AggregateToProteinGroupsParams"> | |
2451 <section name="LabeledTransform"> | |
2452 <conditional name="LabeledTransformLightCond"> | |
2453 <param name="Type" value="Substract"/> | |
2454 <param name="Value" value="2"/> | |
2455 </conditional> | |
2456 <conditional name="LabeledTransformHeavyCond"> | |
2457 <param name="Type" value="Add"/> | |
2458 <param name="Value" value="3"/> | |
2459 </conditional> | |
2460 <conditional name="LabeledTransformRatioCond"> | |
2461 <param name="Type" value="DivideBy"/> | |
2462 <param name="Value" value="4"/> | |
2463 </conditional> | |
2464 </section> | |
2465 <section name="LabeledSingleFilters"> | |
2466 <section name="Light"> | |
2467 <param name="BiggerThan" value="1"/> | |
2468 <param name="SmallerThan" value="2"/> | |
2469 </section> | |
2470 <section name="Heavy"> | |
2471 <param name="BiggerThan" value="1"/> | |
2472 <param name="SmallerThan" value=""/> | |
2473 </section> | |
2474 <section name="Ratio"> | |
2475 <param name="BiggerThan" value=""/> | |
2476 <param name="SmallerThan" value=""/> | |
2477 </section> | |
2478 </section> | |
2479 <section name="LabeledGroupFilters"> | |
2480 <section name="Light"> | |
2481 <param name="Tukey" value="1"/> | |
2482 <param name="Stdev" value="2"/> | |
2483 </section> | |
2484 <section name="Heavy"> | |
2485 <param name="Tukey" value=""/> | |
2486 <param name="Stdev" value="2"/> | |
2487 </section> | |
2488 <section name="Ratio"> | |
2489 <param name="Tukey" value=""/> | |
2490 <param name="Stdev" value=""/> | |
2491 </section> | |
2492 </section> | |
2493 <section name="LabeledAggregation"> | |
2494 <param name="labeledAggregationLight" value="Sum"/> | |
2495 <param name="labeledAggregationHeavy" value="Median"/> | |
2496 <param name="labeledAggregationRatio" value="Median"/> | |
2497 </section> | |
2498 </section> | |
2499 <param name="outputParamfile" value="true"/> | |
2500 <output name="out_paramfile" file="result_6.json"/> | |
2501 </test> | |
2502 </tests> | |
2503 <help> | |
2504 <![CDATA[ | |
2505 What It Does | |
2506 ------------ | |
2507 **Disclaimer** this tool needs a quantAndProt file, which combines the results from ProteinInference and PSMBasedQuantification. | |
2508 | |
2509 After quantification and protein inference are performed, it is known which peptide originated from which protein, as well as the intensity of each peptide. | |
2510 The information available for each peptide now needs to be aggragated for their proteins. | |
2511 | |
2512 This tool performs the aggregation from the peptides to the protein in several steps. | |
2513 The first step for the labeled protein quantification is the aggregation of the differently labeled peptides. Peptides with the same sequence, modifications and | |
2514 charge are aggregated and the ratio between the intensity from the light and heavy version is calculated. | |
2515 The next two aggregation steps are optional. One of them is the aggregation based on charge state. Similarily to the first step, peptides with the same sequence and | |
2516 modifications, but different charge states are being aggregated. | |
2517 The next optional step does the same for peptides with the same sequence, but different modifications. Those steps build upon each other. | |
2518 The last step is the aggregation of all peptides of a protein. The result of each aggregation step is given as a tab separated file. | |
2519 The aggregation is performed according to the given parameters for each step. If an optional aggregation is not performed, the next step takes the result from | |
2520 the prior aggregation. For example, if aggregation by charge and modification are skipped, the protein aggregation gets a collection of peptides, where a peptidesequence can occur with different charge states and modifications. | |
2521 | |
2522 Further Reading | |
2523 --------------- | |
2524 Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html>`_. | |
2525 ]]> | |
2526 </help> | |
2527 </tool> |