-
Notifications
You must be signed in to change notification settings - Fork 16
/
Copy pathnextflow_schema.json
1444 lines (1444 loc) · 85.3 KB
/
nextflow_schema.json
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/nf-core/metaboigniter/master/nextflow_schema.json",
"title": "nf-core/metaboigniter pipeline parameters",
"description": "Pre-processing of mass spectrometry-based metabolomics data",
"type": "object",
"definitions": {
"generic_controls": {
"title": "Generic controls",
"type": "object",
"description": "",
"default": "",
"properties": {
"skip_centroiding": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "If true, the centroiding will be skipped"
},
"skip_alignment": {
"type": "boolean",
"hidden": true,
"description": "If true, the alignment will be skipped"
},
"skip_adduct_detection": {
"type": "boolean",
"hidden": true,
"description": "If true, the adduct detection will be skipped"
},
"requantification": {
"type": "boolean",
"description": "If set to true, requantification will be performed"
},
"identification": {
"type": "boolean",
"description": "If set to true, identification will be performed. Remember to set identification specific parameters"
},
"polarity": {
"type": "string",
"default": "positive",
"enum": ["positive", "negative"],
"description": "Polarity of the data"
},
"parallel_linking": {
"type": "boolean",
"description": "If set, the linking will be performed in parallel, see nr_partitions in linking"
},
"ms2_collection_model": {
"type": "string",
"default": "paired",
"enum": ["separate", "paired"],
"description": "Set wether the MS2 collections have been done on all the MS1 data. If there is a separate MS2 file, set to separate"
}
}
},
"mapping_and_identification": {
"title": "Mapping and Identification",
"type": "object",
"description": "",
"default": "",
"properties": {
"offline_model_ms2query": {
"type": "boolean",
"hidden": true,
"description": "If set, the workflow expects the models to be in models_dir_ms2query"
},
"models_dir_ms2query": {
"type": "string",
"default": "models",
"hidden": true,
"description": "If running offline, this directory has to contain all the files necessary for running MS2Query"
},
"train_library_ms2query": {
"type": "boolean",
"hidden": true,
"description": "If set, the model training will be performed using library_path_ms2query"
},
"library_path_ms2query": {
"type": "string",
"hidden": true,
"description": "path to ms2query library"
},
"mgf_splitmgf_pyopenms": {
"type": "integer",
"default": 1,
"hidden": true,
"description": "If higher than one, parameter files will be split into the selected number. The result of the identification will be perform on each part separately"
},
"mz_tolerance_pyopenms": {
"type": "number",
"default": 20,
"description": "mz tolerance (ppm) for finding C13"
},
"rt_tolerance_pyopenms": {
"type": "number",
"default": 5,
"description": "rt tolerance for finding C13"
},
"annotate_ids_with_subelements_pyopenms": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Store the map index of the sub-feature in the peptide ID."
},
"measure_from_subelements_pyopenms": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches."
},
"ignore_msms_mapping_charge_pyopenms": {
"type": "boolean",
"default": false,
"hidden": true,
"description": "When mapping MS2 precursors to consensus elements, ignore the charge. Specially beneficial in negative mode, if the charges of the consensus features are and spectra are different"
},
"ms2_use_feature_ionization": {
"type": "boolean",
"description": "If set, detected adduct will be used in identification"
},
"ms2_feature_selection": {
"type": "string",
"default": "quality",
"enum": ["quality", "intensity"],
"hidden": true,
"description": "whether feature quality or intensity should be used for feature selection"
},
"ms2_normalized_intensity": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "If ture, normalized intesity will be used for selecting the best feature"
},
"ms2_iterations": {
"type": "integer",
"default": 3,
"hidden": true,
"description": "Number of iterations that should be performed to extract the C13 isotope pattern. If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns"
},
"ms2_ppm_map": {
"type": "number",
"default": 10,
"hidden": true,
"description": "PPM for detecting MS C13"
},
"sirius_project_maxmz": {
"type": "number",
"default": -1,
"hidden": true,
"description": "Just consider compounds with a precursor mz lower or equal this maximum mz. All other compounds in the input file are ignored.="
},
"sirius_project_loglevel": {
"type": "string",
"default": "WARNING",
"hidden": true,
"description": "Set logging level of the Jobs SIRIUS will execute. Valid values: SEVERE, WARNING, INFO, FINER, ALL",
"enum": ["SEVERE", "WARNING", "INFO", "FINER", "ALL"]
},
"sirius_project_ignore_formula": {
"type": "boolean",
"hidden": true,
"description": "Ignore given molecular formula in internal .ms format, while processing."
},
"sirius_sirius_ppm_max": {
"type": "number",
"default": 10,
"description": "Maximum allowed mass deviation in ppm for decomposing masses (ppm)"
},
"sirius_sirius_ppm_max_ms2": {
"type": "number",
"default": 10,
"description": "Maximum allowed mass deviation in ppm for decomposing masses in MS2 (ppm).If not specified, the same value as for the MS1 is used."
},
"sirius_sirius_tree_timeout": {
"type": "number",
"default": 100,
"hidden": true,
"description": "Time out in seconds per fragmentation tree computations. 0 for an infinite amount of time"
},
"sirius_sirius_compound_timeout": {
"type": "number",
"default": 100,
"hidden": true,
"description": "Time out in seconds per fragmentation tree computations. 0 for an infinite amount of time"
},
"sirius_sirius_no_recalibration": {
"type": "boolean",
"description": "Disable recalibration of input spectra"
},
"sirius_sirius_profile": {
"type": "string",
"default": "default",
"enum": ["default", "qtof", "orbitrap", "fticr"],
"description": "Name of the configuration profile"
},
"sirius_sirius_formulas": {
"type": "string",
"description": "Specify the neutral molecular formula of the measured compound to compute its tree or a list of candidate formulas the method should discriminate. Omit this option if you want to consider all possible molecular formulas",
"hidden": true
},
"sirius_sirius_ions_enforced": {
"type": "string",
"description": "The iontype/adduct of the MS/MS data. Example: [M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a comma separated list of adducts.",
"hidden": true
},
"sirius_sirius_candidates": {
"type": "integer",
"default": 10,
"description": "The number of formula candidates in the SIRIUS output"
},
"sirius_sirius_candidates_per_ion": {
"type": "integer",
"default": 1,
"description": "Minimum number of candidates in the output for each ionization. Set to force output of results for each possible ionization, even if not part of highest ranked results."
},
"sirius_sirius_elements_considered": {
"type": "string",
"default": "SBrClBSe",
"description": "Set the allowed elements for rare element detection. Write SBrClBSe to allow the elements S,Br,Cl,B and Se.",
"hidden": true
},
"sirius_sirius_elements_enforced": {
"type": "string",
"default": "CHNOP",
"description": "Enforce elements for molecular formula determination. Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the minimal and maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1-2]. When one number is given then it is interpreted as upper bound.",
"hidden": true
},
"sirius_sirius_no_isotope_score": {
"type": "boolean",
"description": "Disable isotope pattern score.",
"hidden": true
},
"sirius_sirius_no_isotope_filter": {
"type": "boolean",
"description": "Disable molecular formula filter. When filtering is enabled, molecular formulas are excluded if their theoretical isotope pattern does not match the theoretical one, even if their MS/MS pattern has high score.",
"hidden": true
},
"sirius_sirius_ions_considered": {
"type": "string",
"default": "[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-",
"description": "the iontype/adduct of the MS/MS data. Example: [M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a comma separated list of adducts."
},
"sirius_sirius_db": {
"type": "string",
"description": "Search formulas in the Union of the given databases db-name1,db-name2,db-name3. If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE"
},
"sirius_runpassatutto": {
"type": "boolean",
"description": "If set, passatutto will be run"
},
"sirius_fingerid_db": {
"type": "string",
"description": "Search structures in the Union of the given databases db-name1,db-name2,db-name3. If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE"
},
"sirius_sirius_solver": {
"type": "string",
"default": "CLP",
"description": "For GUROBI and CPLEX environment variables need to be configured.",
"hidden": true
},
"sirius_email": {
"type": "string",
"description": "E-mail for your SIRIUS account."
},
"sirius_password": {
"type": "string",
"description": "Password for your SIRIUS account."
},
"sirius_split": {
"type": "boolean",
"description": "If set, SIRIUS will be run in parallel. See mgf_splitmgf_pyopenms parameter for segmentation"
},
"split_consensus_parts": {
"type": "integer",
"default": 20,
"description": "For running MS2 mapping in parallel set this higher than 1"
},
"run_ms2query": {
"type": "boolean",
"description": "If set, MS2Query will be run"
},
"sirius_runfid": {
"type": "boolean",
"description": "If set, FingerID will be run. This has to be run together with run_sirius"
},
"run_sirius": {
"type": "boolean",
"description": "If set SIRIUS will run"
},
"run_umapped_spectra": {
"type": "boolean",
"description": "If set identification will be performed on unmapped MS2 spectra",
"hidden": true
}
}
},
"annotation": {
"title": "Annotation",
"type": "object",
"description": "",
"default": "",
"properties": {
"algorithm_metabolitefeaturedeconvolution_charge_min_metaboliteadductdecharger_openms": {
"type": "integer",
"default": 1,
"hidden": false,
"description": "Minimal possible charge"
},
"algorithm_metabolitefeaturedeconvolution_charge_max_metaboliteadductdecharger_openms": {
"type": "integer",
"default": 1,
"hidden": false,
"description": "Maximal possible charge"
},
"algorithm_metabolitefeaturedeconvolution_charge_span_max_metaboliteadductdecharger_openms": {
"type": "integer",
"hidden": false,
"description": "Maximal range of charges for a single analyte, i.e. observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge",
"default": 1
},
"algorithm_metabolitefeaturedeconvolution_q_try_metaboliteadductdecharger_openms": {
"type": "string",
"default": "feature",
"hidden": false,
"description": "Try different values of charge for each feature according to the above settings ('heuristic' [does not test all charges, just the likely ones] or 'all' ), or leave feature charge untouched ('feature').",
"enum": ["feature", "heuristic", "all"]
},
"algorithm_metabolitefeaturedeconvolution_retention_max_diff_metaboliteadductdecharger_openms": {
"type": "number",
"default": 1,
"hidden": false,
"description": "Maximum allowed RT difference between any two features if their relation shall be determined"
},
"algorithm_metabolitefeaturedeconvolution_retention_max_diff_local_metaboliteadductdecharger_openms": {
"type": "number",
"default": 1,
"hidden": false,
"description": "Maximum allowed RT difference between between two co-features, after adduct shifts have been accounted for (if you do not have any adduct shifts, this value should be equal to 'retention_max_diff', otherwise it should be smaller!)"
},
"algorithm_metabolitefeaturedeconvolution_mass_max_diff_metaboliteadductdecharger_openms": {
"type": "number",
"hidden": false,
"description": "Maximum allowed mass tolerance per feature. Defines a symmetric tolerance window around the feature. When looking at possible feature pairs, the allowed feature-wise errors are combined for consideration of possible adduct shifts. For ppm tolerances, each window is based on the respective observed feature mz (instead of putative experimental mzs causing the observed one)!",
"default": 5
},
"algorithm_metabolitefeaturedeconvolution_unit_metaboliteadductdecharger_openms": {
"type": "string",
"default": "ppm",
"hidden": false,
"description": "Unit of the 'max_difference' parameter",
"enum": ["Da", "ppm"]
},
"algorithm_metabolitefeaturedeconvolution_max_neutrals_metaboliteadductdecharger_openms": {
"type": "integer",
"default": 1,
"hidden": false,
"description": "Maximal number of neutral adducts(q=0) allowed. Add them in the 'potential_adducts' section!"
},
"algorithm_metabolitefeaturedeconvolution_use_minority_bound_metaboliteadductdecharger_openms": {
"type": "boolean",
"default": true,
"hidden": false,
"description": "Prune the considered adduct transitions by transition probabilities."
},
"algorithm_metabolitefeaturedeconvolution_max_minority_bound_metaboliteadductdecharger_openms": {
"type": "integer",
"hidden": false,
"description": "Limits allowed adduct compositions and changes between compositions in the underlying graph optimization problem by introducing a probability-based threshold: the minority bound sets the maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant with maximum charge only containing the most likely adduct otherwise. E.g., for 'charge_max' 4 and 'max_minority_bound' 2 with most probable adduct being H+ and least probable adduct being Na+, this will allow adduct compositions of '2(H+),2(Na+)' but not of '1(H+),3(Na+)'. Further, adduct compositions/changes less likely than '2(H+),2(Na+)' will be discarded as well.",
"default": 1
},
"algorithm_metabolitefeaturedeconvolution_min_rt_overlap_metaboliteadductdecharger_openms": {
"type": "number",
"hidden": false,
"description": "Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)",
"default": 0.66
},
"algorithm_metabolitefeaturedeconvolution_intensity_filter_metaboliteadductdecharger_openms": {
"type": "boolean",
"hidden": false,
"description": "Enable the intensity filter, which will only allow edges between two equally charged features if the intensity of the feature with less likely adducts is smaller than that of the other feature. It is not used for features of different charge."
},
"algorithm_metabolitefeaturedeconvolution_default_map_label_metaboliteadductdecharger_openms": {
"type": "string",
"default": "decharged features",
"hidden": true,
"description": "Label of map in output consensus file where all features are put by default"
},
"adducts_pos": {
"type": "string",
"default": "H:+:0.6 Na:+:0.1 NH4:+:0.1 H-1O-1:+:0.1 H-3O-2:+:0.1",
"description": "possible positive adducts for adduct detection in the format of adduct:charge:probablity"
},
"adducts_neg": {
"type": "string",
"default": "H-1:-:0.8 H-3O-1:-:0.2",
"description": "possible negative adducts for adduct detection in the format of adduct:charge:probablity"
}
}
},
"alignment_and_linking": {
"title": "Alignment and Linking",
"type": "object",
"description": "",
"default": "",
"properties": {
"algorithm_max_num_peaks_considered_mapalignerposeclustering_openms": {
"type": "integer",
"hidden": false,
"description": "The maximal number of peaks/features to be considered per map. To use all, set to '-1'.",
"default": 1000
},
"algorithm_superimposer_mz_pair_max_distance_mapalignerposeclustering_openms": {
"type": "number",
"hidden": false,
"description": "Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing.",
"default": 0.5
},
"algorithm_superimposer_rt_pair_distance_fraction_mapalignerposeclustering_openms": {
"type": "number",
"hidden": true,
"description": "Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min). ",
"default": 0.1
},
"algorithm_superimposer_num_used_points_mapalignerposeclustering_openms": {
"type": "integer",
"hidden": false,
"description": "Maximum number of elements considered in each map (selected by intensity). Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1.",
"default": 2000
},
"algorithm_superimposer_scaling_bucket_size_mapalignerposeclustering_openms": {
"type": "number",
"hidden": true,
"description": "The scaling of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be a bit smaller than the error you would expect from repeated runs.",
"default": 0.005
},
"algorithm_superimposer_shift_bucket_size_mapalignerposeclustering_openms": {
"type": "number",
"hidden": true,
"description": "The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be about the time between consecutive MS scans."
},
"algorithm_superimposer_max_shift_mapalignerposeclustering_openms": {
"type": "number",
"hidden": true,
"description": "Maximal shift which is considered during histogramming (in seconds). This applies for both directions."
},
"algorithm_superimposer_max_scaling_mapalignerposeclustering_openms": {
"type": "number",
"hidden": true,
"description": "Maximal scaling which is considered during histogramming. The minimal scaling is the reciprocal of this."
},
"algorithm_superimposer_dump_buckets_mapalignerposeclustering_openms": {
"type": "string",
"hidden": true,
"description": "[DEBUG] If non-empty, base filename where hash table buckets will be dumped to. A serial number for each invocation will be appended automatically."
},
"algorithm_superimposer_dump_pairs_mapalignerposeclustering_openms": {
"type": "string",
"hidden": true,
"description": "[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!). A serial number for each invocation will be appended automatically."
},
"algorithm_pairfinder_second_nearest_gap_mapalignerposeclustering_openms": {
"type": "number",
"hidden": true,
"description": "Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself."
},
"algorithm_pairfinder_use_identifications_mapalignerposeclustering_openms": {
"type": "boolean",
"hidden": true,
"description": "Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)."
},
"algorithm_pairfinder_ignore_charge_mapalignerposeclustering_openms": {
"type": "boolean",
"hidden": false,
"description": "false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state"
},
"algorithm_pairfinder_ignore_adduct_mapalignerposeclustering_openms": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts"
},
"algorithm_pairfinder_distance_rt_max_difference_mapalignerposeclustering_openms": {
"type": "number",
"hidden": false,
"description": "Never pair features with a larger RT distance (in seconds).",
"default": 100.0
},
"algorithm_pairfinder_distance_rt_exponent_mapalignerposeclustering_openms": {
"type": "number",
"hidden": true,
"description": "Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)"
},
"algorithm_pairfinder_distance_rt_weight_mapalignerposeclustering_openms": {
"type": "number",
"hidden": true,
"description": "Final RT distances are weighted by this factor"
},
"algorithm_pairfinder_distance_mz_max_difference_mapalignerposeclustering_openms": {
"type": "number",
"hidden": false,
"description": "Never pair features with larger m/z distance (unit defined by 'unit')",
"default": 0.3
},
"algorithm_pairfinder_distance_mz_unit_mapalignerposeclustering_openms": {
"type": "string",
"default": "Da",
"hidden": false,
"description": "Unit of the 'max_difference' parameter",
"enum": ["Da", "ppm"]
},
"algorithm_pairfinder_distance_mz_exponent_mapalignerposeclustering_openms": {
"type": "number",
"hidden": true,
"description": "Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)"
},
"algorithm_pairfinder_distance_mz_weight_mapalignerposeclustering_openms": {
"type": "number",
"hidden": true,
"description": "Final m/z distances are weighted by this factor"
},
"algorithm_pairfinder_distance_intensity_exponent_mapalignerposeclustering_openms": {
"type": "number",
"hidden": true,
"description": "Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)"
},
"algorithm_pairfinder_distance_intensity_weight_mapalignerposeclustering_openms": {
"type": "number",
"hidden": true,
"description": "Final intensity distances are weighted by this factor"
},
"algorithm_pairfinder_distance_intensity_log_transform_mapalignerposeclustering_openms": {
"type": "string",
"default": "disabled",
"hidden": true,
"description": "Log-transform intensities? If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))",
"enum": ["enabled", "disabled"]
},
"algorithm_mz_unit_featurelinkerunlabeledkd_openms": {
"type": "string",
"default": "ppm",
"hidden": false,
"description": "Unit of m/z tolerance",
"enum": ["ppm", "Da"]
},
"algorithm_nr_partitions_featurelinkerunlabeledkd_openms": {
"type": "integer",
"hidden": false,
"description": "Number of partitions in m/z space",
"default": 100
},
"algorithm_warp_enabled_featurelinkerunlabeledkd_openms": {
"type": "boolean",
"default": true,
"hidden": false,
"description": "Whether or not to internally warp feature RTs using LOWESS transformation before linking (reported RTs in results will always be the original RTs)"
},
"algorithm_warp_rt_tol_featurelinkerunlabeledkd_openms": {
"type": "number",
"hidden": false,
"description": "Width of RT tolerance window (sec)",
"default": 100.0
},
"algorithm_warp_mz_tol_featurelinkerunlabeledkd_openms": {
"type": "number",
"hidden": false,
"description": "m/z tolerance (in ppm or Da)",
"default": 5.0
},
"algorithm_warp_max_pairwise_log_fc_featurelinkerunlabeledkd_openms": {
"type": "number",
"default": 0.5,
"hidden": true,
"description": "Maximum absolute log10 fold change between two compatible signals during compatibility graph construction. Two signals from different maps will not be connected by an edge in the compatibility graph if absolute log fold change exceeds this limit (they might still end up in the same connected component, however). Note: this does not limit fold changes in the linking stage, only during RT alignment, where we try to find high-quality alignment anchor points. Setting this to a value < 0 disables the FC check."
},
"algorithm_warp_min_rel_cc_size_featurelinkerunlabeledkd_openms": {
"type": "number",
"hidden": true,
"description": "Only connected components containing compatible features from at least max(2, (warp_min_occur * number_of_input_maps)) input maps are considered for computing the warping function",
"default": 0.5
},
"algorithm_warp_max_nr_conflicts_featurelinkerunlabeledkd_openms": {
"type": "integer",
"hidden": true,
"description": "Allow up to this many conflicts (features from the same map) per connected component to be used for alignment (-1 means allow any number of conflicts)",
"default": 0
},
"algorithm_link_rt_tol_featurelinkerunlabeledkd_openms": {
"type": "number",
"hidden": false,
"description": "Width of RT tolerance window (sec)",
"default": 30
},
"algorithm_link_mz_tol_featurelinkerunlabeledkd_openms": {
"type": "number",
"hidden": false,
"description": "m/z tolerance (in ppm or Da)",
"default": 10
},
"algorithm_link_charge_merging_featurelinkerunlabeledkd_openms": {
"type": "string",
"default": "With_charge_zero",
"hidden": false,
"description": "whether to disallow charge mismatches (Identical), allow to link charge zero (i.e., unknown charge state) with every charge state, or disregard charges (Any).",
"enum": ["Identical", "With_charge_zero", "Any"]
},
"algorithm_link_adduct_merging_featurelinkerunlabeledkd_openms": {
"type": "string",
"default": "Any",
"hidden": false,
"description": "whether to only allow the same adduct for linking (Identical), also allow linking features with adduct-free ones, or disregard adducts (Any).",
"enum": ["Identical", "With_unknown_adducts", "Any"]
},
"algorithm_distance_rt_exponent_featurelinkerunlabeledkd_openms": {
"type": "number",
"hidden": true,
"description": "Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)",
"default": 1
},
"algorithm_distance_rt_weight_featurelinkerunlabeledkd_openms": {
"type": "number",
"hidden": true,
"description": "Final RT distances are weighted by this factor",
"default": 1
},
"algorithm_distance_mz_exponent_featurelinkerunlabeledkd_openms": {
"type": "number",
"hidden": true,
"description": "Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)",
"default": 2
},
"algorithm_distance_mz_weight_featurelinkerunlabeledkd_openms": {
"type": "number",
"hidden": true,
"description": "Final m/z distances are weighted by this factor",
"default": 1
},
"algorithm_distance_intensity_exponent_featurelinkerunlabeledkd_openms": {
"type": "number",
"hidden": true,
"description": "Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)",
"default": 1
},
"algorithm_distance_intensity_weight_featurelinkerunlabeledkd_openms": {
"type": "number",
"hidden": true,
"description": "Final intensity distances are weighted by this factor",
"default": 1
},
"algorithm_distance_intensity_log_transform_featurelinkerunlabeledkd_openms": {
"type": "string",
"default": "enabled",
"hidden": true,
"description": "Log-transform intensities? If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))",
"enum": ["enabled", "disabled"]
},
"algorithm_lowess_span_featurelinkerunlabeledkd_openms": {
"type": "number",
"hidden": true,
"description": "Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing). Choosing this parameter in the range .2 to .8 usually results in a good fit.",
"default": 0.666666666666667
},
"algorithm_lowess_num_iterations_featurelinkerunlabeledkd_openms": {
"type": "integer",
"hidden": true,
"description": "Number of robustifying iterations for lowess fitting.",
"default": 3
},
"algorithm_lowess_delta_featurelinkerunlabeledkd_openms": {
"type": "number",
"default": -1,
"hidden": true,
"description": "Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input, e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this."
},
"algorithm_lowess_interpolation_type_featurelinkerunlabeledkd_openms": {
"type": "string",
"default": "cspline",
"hidden": true,
"description": "Method to use for interpolation between datapoints computed by lowess. 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation",
"enum": ["linear", "cspline", "akima"]
},
"algorithm_lowess_extrapolation_type_featurelinkerunlabeledkd_openms": {
"type": "string",
"default": "four-point-linear",
"hidden": true,
"description": "Method to use for extrapolation outside the data range. 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation.",
"enum": ["two-point-linear", "four-point-linear", "global-linear"]
},
"keep_subelements_featurelinkerunlabeledkd_openms": {
"type": "boolean",
"hidden": true,
"description": "For consensusXML input only: If set, the sub-features of the inputs are transferred to the output."
},
"invert_maprttransformer_openms": {
"type": "boolean",
"hidden": true,
"description": "Invert transformation (approximatively) before applying it"
},
"store_original_rt_maprttransformer_openms": {
"type": "boolean",
"hidden": true,
"description": "Store the original retention times (before transformation) as meta data in the output file"
},
"model_type_maprttransformer_openms": {
"type": "string",
"default": "none",
"hidden": true,
"description": "Type of model",
"enum": ["none", "linear", "b_spline", "lowess", "interpolated"]
},
"model_linear_symmetric_regression_maprttransformer_openms": {
"type": "boolean",
"hidden": true,
"description": "Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'."
},
"model_linear_x_weight_maprttransformer_openms": {
"type": "string",
"default": "x",
"hidden": true,
"description": "Weight x values",
"enum": ["1/x", "1/x2", "ln(x)", "x"]
},
"model_linear_y_weight_maprttransformer_openms": {
"type": "string",
"default": "y",
"hidden": true,
"description": "Weight y values",
"enum": ["1/y", "1/y2", "ln(y)", "y"]
},
"model_linear_x_datum_min_maprttransformer_openms": {
"type": "number",
"default": 1e-15,
"hidden": true,
"description": "Minimum x value"
},
"model_linear_x_datum_max_maprttransformer_openms": {
"type": "number",
"default": 1000000000000000,
"hidden": true,
"description": "Maximum x value"
},
"model_linear_y_datum_min_maprttransformer_openms": {
"type": "number",
"default": 1e-15,
"hidden": true,
"description": "Minimum y value"
},
"model_linear_y_datum_max_maprttransformer_openms": {
"type": "number",
"default": 1000000000000000,
"hidden": true,
"description": "Maximum y value"
},
"model_b_spline_wavelength_maprttransformer_openms": {
"type": "number",
"hidden": true,
"description": "Determines the amount of smoothing by setting the number of nodes for the B-spline. The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points."
},
"model_b_spline_num_nodes_maprttransformer_openms": {
"type": "integer",
"hidden": true,
"description": "Number of nodes for B-spline fitting. Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing."
},
"model_b_spline_extrapolate_maprttransformer_openms": {
"type": "string",
"default": "linear",
"hidden": true,
"description": "Method to use for extrapolation beyond the original data range. 'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range).",
"enum": ["linear", "b_spline", "constant", "global_linear"]
},
"model_b_spline_boundary_condition_maprttransformer_openms": {
"type": "integer",
"hidden": true,
"description": "Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)"
},
"model_lowess_span_maprttransformer_openms": {
"type": "number",
"hidden": true,
"description": "Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing). Choosing this parameter in the range .2 to .8 usually results in a good fit."
},
"model_lowess_num_iterations_maprttransformer_openms": {
"type": "integer",
"hidden": true,
"description": "Number of robustifying iterations for lowess fitting."
},
"model_lowess_delta_maprttransformer_openms": {
"type": "number",
"default": -1,
"hidden": true,
"description": "Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input, e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this."
},
"model_lowess_interpolation_type_maprttransformer_openms": {
"type": "string",
"default": "cspline",
"hidden": true,
"description": "Method to use for interpolation between datapoints computed by lowess. 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation",
"enum": ["linear", "cspline", "akima"]
},
"model_lowess_extrapolation_type_maprttransformer_openms": {
"type": "string",
"default": "four-point-linear",
"hidden": true,
"description": "Method to use for extrapolation outside the data range. 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation.",
"enum": ["two-point-linear", "four-point-linear", "global-linear"]
},
"model_interpolated_interpolation_type_maprttransformer_openms": {
"type": "string",
"default": "cspline",
"hidden": true,
"description": "Type of interpolation to apply.",
"enum": ["linear", "cspline", "akima"]
},
"model_interpolated_extrapolation_type_maprttransformer_openms": {
"type": "string",
"default": "two-point-linear",
"hidden": true,
"description": "Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model. Note that global-linear may not be continuous at the border.",
"enum": ["two-point-linear", "four-point-linear", "global-linear"]
}
}
},
"re_quantification": {
"type": "object",
"title": "Re-Quantification",
"description": "",
"default": "",
"properties": {
"extract_mz_window_featurefindermetaboident_openms": {
"type": "number",
"hidden": false,
"description": "m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)"
},
"extract_rt_window_featurefindermetaboident_openms": {
"type": "number",
"hidden": true,
"description": "RT window size (in sec.) for chromatogram extraction. If set, this parameter takes precedence over 'extract:rt_quantile'."
},
"extract_n_isotopes_featurefindermetaboident_openms": {
"type": "integer",
"hidden": false,
"description": "Number of isotopes to include in each peptide assay."
},
"extract_isotope_pmin_featurefindermetaboident_openms": {
"type": "number",
"hidden": true,
"description": "Minimum probability for an isotope to be included in the assay for a peptide. If set, this parameter takes precedence over 'extract:n_isotopes'."
},
"detect_peak_width_featurefindermetaboident_openms": {
"type": "number",
"hidden": false,
"description": "Expected elution peak width in seconds, for smoothing (Gauss filter). Also determines the RT extration window, unless set explicitly via 'extract:rt_window'."
},
"detect_min_peak_width_featurefindermetaboident_openms": {
"type": "number",
"hidden": true,
"description": "Minimum elution peak width. Absolute value in seconds if 1 or greater, else relative to 'peak_width'."
},
"detect_signal_to_noise_featurefindermetaboident_openms": {
"type": "number",
"hidden": true,
"description": "Signal-to-noise threshold for OpenSWATH feature detection"
},
"model_type_featurefindermetaboident_openms": {
"type": "string",
"default": "symmetric",
"hidden": false,
"description": "Type of elution model to fit to features",
"enum": ["symmetric", "asymmetric", "none"]
},
"model_add_zeros_featurefindermetaboident_openms": {
"type": "number",
"hidden": true,
"description": "Add zero-intensity points outside the feature range to constrain the model fit. This parameter sets the weight given to these points during model fitting; '0' to disable."
},
"model_unweighted_fit_featurefindermetaboident_openms": {
"type": "boolean",
"hidden": true,
"description": "Suppress weighting of mass traces according to theoretical intensities when fitting elution models"
},
"model_no_imputation_featurefindermetaboident_openms": {
"type": "boolean",
"hidden": true,
"description": "If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate"
},
"model_each_trace_featurefindermetaboident_openms": {
"type": "boolean",
"hidden": true,
"description": "Fit elution model to each individual mass trace"
},
"model_check_min_area_featurefindermetaboident_openms": {
"type": "number",
"hidden": true,
"description": "Lower bound for the area under the curve of a valid elution model"
},
"model_check_boundaries_featurefindermetaboident_openms": {
"type": "number",
"hidden": true,
"description": "Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting"
},
"model_check_width_featurefindermetaboident_openms": {
"type": "number",
"hidden": true,
"description": "Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores. '0' to disable. Not applied to individual mass traces (parameter 'each_trace')."
},
"model_check_asymmetry_featurefindermetaboident_openms": {
"type": "number",
"hidden": true,
"description": "Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores. '0' to disable. Not applied to individual mass traces (parameter 'each_trace')."
},
"emgscoring_max_iteration_featurefindermetaboident_openms": {
"type": "integer",
"hidden": false,
"description": "Maximum number of iterations for EMG fitting."
},
"emgscoring_init_mom_featurefindermetaboident_openms": {
"type": "boolean",
"hidden": false,
"description": "Alternative initial parameters for fitting through method of moments."
}
}
},
"quantification": {
"title": "Quantification",
"type": "object",
"description": "",
"default": "",
"properties": {
"algorithm_signal_to_noise_peakpickerhires_openms": {
"type": "number",
"hidden": false,
"description": "Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)"
},
"algorithm_spacing_difference_gap_peakpickerhires_openms": {
"type": "number",
"hidden": true,
"description": "The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms."
},
"algorithm_spacing_difference_peakpickerhires_openms": {
"type": "number",
"hidden": true,
"description": "Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points. If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms."
},
"algorithm_missing_peakpickerhires_openms": {
"type": "integer",
"hidden": true,
"description": "Maximum number of missing points allowed when extending a peak to the left or to the right. A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms."
},
"algorithm_report_fwhm_peakpickerhires_openms": {
"type": "boolean",
"hidden": true,
"description": "Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak."
},
"algorithm_report_fwhm_unit_peakpickerhires_openms": {
"type": "string",
"default": "relative",
"hidden": true,
"description": "Unit of FWHM. Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms).",
"enum": ["relative", "absolute"]
},
"algorithm_signaltonoise_max_intensity_peakpickerhires_openms": {
"type": "integer",
"hidden": true,
"description": "maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N."
},
"algorithm_signaltonoise_auto_max_stdev_factor_peakpickerhires_openms": {
"type": "number",
"hidden": true,
"description": "parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev"
},
"algorithm_signaltonoise_auto_max_percentile_peakpickerhires_openms": {
"type": "integer",
"hidden": true,
"description": "parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile"
},
"algorithm_signaltonoise_auto_mode_peakpickerhires_openms": {
"type": "integer",
"hidden": true,
"description": "method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method"
},
"algorithm_signaltonoise_win_len_peakpickerhires_openms": {
"type": "number",
"hidden": true,
"description": "window length in Thomson"
},
"algorithm_signaltonoise_bin_count_peakpickerhires_openms": {
"type": "integer",
"hidden": true,
"description": "number of bins for intensity values"
},
"algorithm_signaltonoise_min_required_elements_peakpickerhires_openms": {
"type": "integer",
"hidden": true,
"description": "minimum number of elements required in a window (otherwise it is considered sparse)"
},
"algorithm_signaltonoise_noise_for_empty_window_peakpickerhires_openms": {
"type": "number",
"default": 100000000000000000000,
"hidden": true,
"description": "noise value used for sparse windows"
},
"algorithm_common_noise_threshold_int_featurefindermetabo_openms": {