Mercurial > repos > galaxyp > proteomiqon_labeledproteinquantification

comparison labeledproteinquantification.xml @ 0:cbdfdca98db3 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification commit eda2d62c81b38ed3975482d0198e3dd75ff1d74f"
author galaxyp
date Thu, 16 Sep 2021 21:11:34 +0000
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-1:000000000000 0:cbdfdca98db3
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>