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comparison workflows/DIA_SpecLib_Quant.workflow @ 7:b4f6df8fa89b draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
author galaxyp
date Wed, 01 Oct 2025 22:20:54 +0000
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comparison
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6:59fec1e2a6c3 7:b4f6df8fa89b
1 # Workflow: DIA_SpecLib_Quant
2
3 crystalc.run-crystalc=false
4 database.decoy-tag=rev_
5 diann.channel-normalization-strategy=0
6 diann.cmd-opts=
7 diann.generate-msstats=true
8 diann.heavy=
9 diann.library=
10 diann.light=
11 diann.medium=
12 diann.min-site-prob=0.75
13 diann.mod-tag=
14 diann.q-value=0.01
15 diann.quantification-strategy=3
16 diann.quantification-strategy-2=2
17 diann.run-dia-nn=true
18 diann.run-dia-plex=false
19 diann.run-specific-protein-q-value=false
20 diann.unrelated-runs=false
21 diann.use-predicted-spectra=false
22 diatracer.corr-threshold=0.3
23 diatracer.delta-apex-im=0.01
24 diatracer.delta-apex-rt=3
25 diatracer.mass-defect-filter=true
26 diatracer.mass-defect-offset=0.1
27 diatracer.rf-max=500
28 diatracer.run-diatracer=false
29 diatracer.write-intermediate-files=false
30 diaumpire.AdjustFragIntensity=true
31 diaumpire.BoostComplementaryIon=false
32 diaumpire.CorrThreshold=0
33 diaumpire.DeltaApex=0.2
34 diaumpire.ExportPrecursorPeak=false
35 diaumpire.Q1=true
36 diaumpire.Q2=true
37 diaumpire.Q3=true
38 diaumpire.RFmax=500
39 diaumpire.RPmax=25
40 diaumpire.RTOverlap=0.3
41 diaumpire.SE.EstimateBG=false
42 diaumpire.SE.IsoPattern=0.3
43 diaumpire.SE.MS1PPM=10
44 diaumpire.SE.MS2PPM=20
45 diaumpire.SE.MS2SN=1.1
46 diaumpire.SE.MassDefectFilter=true
47 diaumpire.SE.MassDefectOffset=0.1
48 diaumpire.SE.NoMissedScan=1
49 diaumpire.SE.SN=1.1
50 diaumpire.run-diaumpire=false
51 fpop.coadaptr.fpop.fpop_masses=
52 fpop.coadaptr.fpop.run-fpop-coadaptr=false
53 fpop.fragpipe.fpop.fpop-tmt=false
54 fpop.fragpipe.fpop.label_control=
55 fpop.fragpipe.fpop.label_fpop=
56 fpop.fragpipe.fpop.region_size=1
57 fpop.fragpipe.fpop.run-fpop=false
58 fpop.fragpipe.fpop.subtract-control=false
59 freequant.mz-tol=10
60 freequant.rt-tol=0.4
61 freequant.run-freequant=false
62 ionquant.excludemods=
63 ionquant.formula=
64 ionquant.heavy=
65 ionquant.imtol=0.05
66 ionquant.ionfdr=0.01
67 ionquant.light=
68 ionquant.locprob=0.75
69 ionquant.maxlfq=1
70 ionquant.mbr=0
71 ionquant.mbrimtol=0.05
72 ionquant.mbrmincorr=0
73 ionquant.mbrrttol=1
74 ionquant.mbrtoprun=10
75 ionquant.medium=
76 ionquant.minfreq=0
77 ionquant.minions=1
78 ionquant.minisotopes=1
79 ionquant.minscans=3
80 ionquant.mztol=10
81 ionquant.normalization=1
82 ionquant.peptidefdr=1
83 ionquant.proteinfdr=1
84 ionquant.requantify=1
85 ionquant.rttol=0.4
86 ionquant.run-ionquant=true
87 ionquant.tp=0
88 ionquant.uniqueness=0
89 ionquant.use-labeling=false
90 ionquant.use-lfq=true
91 ionquant.writeindex=0
92 msbooster.find-best-im-model=false
93 msbooster.find-best-rt-model=false
94 msbooster.find-best-spectra-model=false
95 msbooster.fragmentation-type=0
96 msbooster.im-model=DIA-NN
97 msbooster.koina-url=
98 msbooster.predict-im=true
99 msbooster.predict-rt=true
100 msbooster.predict-spectra=true
101 msbooster.rt-model=DIA-NN
102 msbooster.run-msbooster=true
103 msbooster.spectra-model=DIA-NN
104 msbooster.spectral-library-path=
105 msfragger.Y_type_masses=
106 msfragger.activation_types=all
107 msfragger.allowed_missed_cleavage_1=1
108 msfragger.allowed_missed_cleavage_2=1
109 msfragger.analyzer_types=all
110 msfragger.calibrate_mass=2
111 msfragger.check_spectral_files=false
112 msfragger.clip_nTerm_M=true
113 msfragger.deisotope=1
114 msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
115 msfragger.deneutralloss=1
116 msfragger.diagnostic_fragments=
117 msfragger.diagnostic_intensity_filter=0
118 msfragger.digest_max_length=50
119 msfragger.digest_min_length=7
120 msfragger.fragment_ion_series=b,y
121 msfragger.fragment_mass_tolerance=20
122 msfragger.fragment_mass_units=1
123 msfragger.group_variable=0
124 msfragger.intensity_transform=0
125 msfragger.ion_series_definitions=
126 msfragger.isotope_error=0/1/2
127 msfragger.labile_search_mode=off
128 msfragger.localize_delta_mass=false
129 msfragger.mass_diff_to_variable_mod=0
130 msfragger.mass_offsets=0
131 msfragger.mass_offsets_detailed=
132 msfragger.max_fragment_charge=2
133 msfragger.max_variable_mods_combinations=5000
134 msfragger.max_variable_mods_per_peptide=3
135 msfragger.min_fragments_modelling=2
136 msfragger.min_matched_fragments=4
137 msfragger.min_sequence_matches=2
138 msfragger.minimum_peaks=15
139 msfragger.minimum_ratio=0.00
140 msfragger.misc.fragger.clear-mz-hi=0
141 msfragger.misc.fragger.clear-mz-lo=0
142 msfragger.misc.fragger.digest-mass-hi=5000
143 msfragger.misc.fragger.digest-mass-lo=500
144 msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
145 msfragger.misc.fragger.enzyme-dropdown-2=null
146 msfragger.misc.fragger.precursor-charge-hi=4
147 msfragger.misc.fragger.precursor-charge-lo=2
148 msfragger.misc.fragger.remove-precursor-range-hi=1.5
149 msfragger.misc.fragger.remove-precursor-range-lo=-1.5
150 msfragger.misc.slice-db=1
151 msfragger.num_enzyme_termini=2
152 msfragger.output_format=pepXML_pin
153 msfragger.output_max_expect=50
154 msfragger.output_report_topN=1
155 msfragger.output_report_topN_dda_plus=5
156 msfragger.output_report_topN_dia1=5
157 msfragger.override_charge=false
158 msfragger.precursor_mass_lower=-20
159 msfragger.precursor_mass_mode=selected
160 msfragger.precursor_mass_units=1
161 msfragger.precursor_mass_upper=20
162 msfragger.precursor_true_tolerance=20
163 msfragger.precursor_true_units=1
164 msfragger.remainder_fragment_masses=
165 msfragger.remove_precursor_peak=1
166 msfragger.report_alternative_proteins=true
167 msfragger.require_precursor=true
168 msfragger.restrict_deltamass_to=all
169 msfragger.reuse_dia_fragment_peaks=false
170 msfragger.run-msfragger=true
171 msfragger.search_enzyme_cut_1=KR
172 msfragger.search_enzyme_cut_2=
173 msfragger.search_enzyme_name_1=stricttrypsin
174 msfragger.search_enzyme_name_2=null
175 msfragger.search_enzyme_nocut_1=
176 msfragger.search_enzyme_nocut_2=
177 msfragger.search_enzyme_sense_1=C
178 msfragger.search_enzyme_sense_2=C
179 msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
180 msfragger.table.var-mods=15.9949,M,true,1; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 0.0,site_06,false,1; 0.0,site_07,false,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
181 msfragger.track_zero_topN=0
182 msfragger.use_all_mods_in_first_search=false
183 msfragger.use_detailed_offsets=false
184 msfragger.use_topN_peaks=1000
185 msfragger.write_calibrated_mzml=false
186 msfragger.zero_bin_accept_expect=0
187 msfragger.zero_bin_mult_expect=1
188 opair.activation1=HCD
189 opair.activation2=ETD
190 opair.allowed_sites=
191 opair.filterOxonium=true
192 opair.glyco_db=
193 opair.max_glycans=4
194 opair.max_isotope_error=2
195 opair.min_isotope_error=0
196 opair.ms1_tol=20
197 opair.ms2_tol=20
198 opair.oxonium_filtering_file=
199 opair.oxonium_minimum_intensity=0.05
200 opair.reverse_scan_order=false
201 opair.run-opair=false
202 opair.single_scan_type=false
203 peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
204 peptide-prophet.combine-pepxml=false
205 peptide-prophet.run-peptide-prophet=false
206 percolator.cmd-opts=--no-terminate --post-processing-tdc --subset-max-train 500000
207 percolator.keep-tsv-files=false
208 percolator.min-prob=0.7
209 percolator.run-percolator=true
210 phi-report.dont-use-prot-proph-file=false
211 phi-report.filter=--picked --prot 0.01 --minPepLen 8
212 phi-report.pep-level-summary=false
213 phi-report.print-decoys=false
214 phi-report.prot-level-summary=false
215 phi-report.remove-contaminants=false
216 phi-report.run-report=true
217 protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5
218 protein-prophet.run-protein-prophet=true
219 ptmprophet.cmdline=
220 ptmprophet.override-defaults=false
221 ptmprophet.run-ptmprophet=false
222 ptmshepherd.adv_params=false
223 ptmshepherd.annotation-common=false
224 ptmshepherd.annotation-custom=false
225 ptmshepherd.annotation-glyco=false
226 ptmshepherd.annotation-unimod=true
227 ptmshepherd.annotation_file=
228 ptmshepherd.annotation_tol=0.01
229 ptmshepherd.cap_y_ions=
230 ptmshepherd.decoy_type=1
231 ptmshepherd.diag_ions=
232 ptmshepherd.diagmine_diagMinFoldChange=3.0
233 ptmshepherd.diagmine_diagMinSpecDiff=25
234 ptmshepherd.diagmine_fragMinFoldChange=3.0
235 ptmshepherd.diagmine_fragMinPropensity=12.5
236 ptmshepherd.diagmine_fragMinSpecDiff=25
237 ptmshepherd.diagmine_minIonsPerSpec=2
238 ptmshepherd.diagmine_minPeps=25
239 ptmshepherd.diagmine_pepMinFoldChange=3.0
240 ptmshepherd.diagmine_pepMinSpecDiff=25
241 ptmshepherd.glyco_fdr=1.00
242 ptmshepherd.glyco_isotope_max=3
243 ptmshepherd.glyco_isotope_min=-1
244 ptmshepherd.glyco_ppm_tol=50
245 ptmshepherd.glycodatabase=
246 ptmshepherd.histo_smoothbins=2
247 ptmshepherd.iontype_a=false
248 ptmshepherd.iontype_b=true
249 ptmshepherd.iontype_c=true
250 ptmshepherd.iontype_x=false
251 ptmshepherd.iontype_y=true
252 ptmshepherd.iontype_z=true
253 ptmshepherd.iterloc_maxEpoch=100
254 ptmshepherd.iterloc_mode=false
255 ptmshepherd.localization_allowed_res=
256 ptmshepherd.n_glyco=true
257 ptmshepherd.normalization-psms=true
258 ptmshepherd.normalization-scans=false
259 ptmshepherd.output_extended=false
260 ptmshepherd.peakpicking_mass_units=0
261 ptmshepherd.peakpicking_minPsm=10
262 ptmshepherd.peakpicking_promRatio=0.3
263 ptmshepherd.peakpicking_width=0.002
264 ptmshepherd.precursor_mass_units=0
265 ptmshepherd.precursor_tol=0.01
266 ptmshepherd.print_decoys=false
267 ptmshepherd.print_full_glyco_params=false
268 ptmshepherd.prob_mass=0.5
269 ptmshepherd.remainder_masses=
270 ptmshepherd.remove_glycan_delta_mass=true
271 ptmshepherd.run-shepherd=false
272 ptmshepherd.run_diagextract_mode=false
273 ptmshepherd.run_diagmine_mode=false
274 ptmshepherd.run_glyco_mode=false
275 ptmshepherd.spectra_condPeaks=150
276 ptmshepherd.spectra_condRatio=0.0001
277 ptmshepherd.spectra_maxPrecursorCharge=4
278 ptmshepherd.spectra_maxfragcharge=2
279 ptmshepherd.spectra_ppmtol=20
280 ptmshepherd.varmod_masses=
281 quantitation.run-label-free-quant=false
282 run-psm-validation=true
283 run-validation-tab=true
284 saintexpress.cmd-opts=
285 saintexpress.max-replicates=10
286 saintexpress.run-saint-express=false
287 saintexpress.virtual-controls=100
288 skyline.run-skyline=false
289 skyline.skyline=false
290 skyline.skyline-custom=false
291 skyline.skyline-custom-path=
292 skyline.skyline-daily=true
293 skyline.skyline-fragment-tolerance=10
294 skyline.skyline-mods-mode=Default
295 skyline.skyline-precursor-tolerance=10
296 skyline.use-ssl=false
297 speclibgen.convert-pepxml=true
298 speclibgen.convert-psm=false
299 speclibgen.easypqp.extras.max_delta_ppm=15
300 speclibgen.easypqp.extras.max_delta_unimod=0.02
301 speclibgen.easypqp.extras.max_glycan_qval=1
302 speclibgen.easypqp.extras.rt_lowess_fraction=0
303 speclibgen.easypqp.fragment.a=false
304 speclibgen.easypqp.fragment.b=true
305 speclibgen.easypqp.fragment.c=false
306 speclibgen.easypqp.fragment.x=false
307 speclibgen.easypqp.fragment.y=true
308 speclibgen.easypqp.fragment.z=false
309 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
310 speclibgen.easypqp.labile_mode=Regular (not glyco)
311 speclibgen.easypqp.neutral_loss=false
312 speclibgen.easypqp.rt-cal=noiRT
313 speclibgen.easypqp.select-file.text=
314 speclibgen.easypqp.select-im-file.text=
315 speclibgen.keep-intermediate-files=false
316 speclibgen.run-speclibgen=true
317 tab-run.delete_calibrated_mzml=false
318 tab-run.delete_temp_files=false
319 tab-run.export_matched_fragments=false
320 tab-run.sub_mzml_prob_threshold=0.5
321 tab-run.write_sub_mzml=false
322 tmtintegrator.add_Ref=-1
323 tmtintegrator.aggregation_method=0
324 tmtintegrator.allow_overlabel=true
325 tmtintegrator.allow_unlabeled=true
326 tmtintegrator.best_psm=true
327 tmtintegrator.channel_num=TMT-6
328 tmtintegrator.extraction_tool=IonQuant
329 tmtintegrator.glyco_qval=-1
330 tmtintegrator.groupby=-1
331 tmtintegrator.log2transformed=true
332 tmtintegrator.max_pep_prob_thres=0
333 tmtintegrator.min_ntt=0
334 tmtintegrator.min_pep_prob=0.9
335 tmtintegrator.min_percent=0.05
336 tmtintegrator.min_purity=0.5
337 tmtintegrator.min_resolution=0
338 tmtintegrator.min_site_prob=-1
339 tmtintegrator.min_snr=0
340 tmtintegrator.mod_tag=none
341 tmtintegrator.ms1_int=true
342 tmtintegrator.outlier_removal=true
343 tmtintegrator.philosopher-msstats=false
344 tmtintegrator.print_RefInt=false
345 tmtintegrator.prot_exclude=none
346 tmtintegrator.prot_norm=0
347 tmtintegrator.psm_norm=false
348 tmtintegrator.quant_level=2
349 tmtintegrator.ref_d_tag=Pool
350 tmtintegrator.ref_tag=Bridge
351 tmtintegrator.run-tmtintegrator=false
352 tmtintegrator.tolerance=20
353 tmtintegrator.top3_pep=true
354 tmtintegrator.unique_gene=0
355 tmtintegrator.unique_pep=false
356 tmtintegrator.use_glycan_composition=false
357 workflow.description=<p style\="margin-top\: 0">Complete workflow for DIA analysis using spectral library building and quantification using DIA-NN.</p>\n<p style\="margin-top\: 0"></p>\n<p style\="margin-top\: 0">Spectral library can be built from DDA data and/or DIA data, with direct identification from DIA data using MSFragger-DIA. All data are processed together using MSFragger (in DDA or DIA mode, respectively) - MSBooster - Percolator - ProteinProphet (Philosopher) - EasyPQP. The library is filtered to 1% FDR at the protein and peptide levels. DIA files annotated as 'DIA-Quant' are used for quantification only (i.e. not used for spectral library building). If building the library from fractionated DDA data only, in EasyPQP tab change RT Calibration option to "ciRT", or "iRT" if using organisms other than yeast or human (requires iRT peptides).</p>\n<p style\="margin-top\: 0"></p>\n<p style\="margin-top\: 0">Supports DDA RAW/.d files, mzML, and MGF files. DIA files with staggered windows should be mzML files demultiplexed using Proteowizard. For quantification using DIA-NN, Thermo/Sciex DIA files should be in mzML format, and .d for Bruker's timsTOF. diaPASEF DIA data will only be used for quantification (i.e. automatically considered as 'DIA-Quant' data type).</p>
358 workflow.input.data-type.im-ms=false
359 workflow.input.data-type.regular-ms=true
360 workflow.misc.save-sdrf=true
361 workflow.misc.sdrf-type=Default
362 workflow.saved-with-ver=23.0-build14