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comparison workflows/Basic-Search.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: Basic-Search
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=false
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=1
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=2
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=2
108 msfragger.allowed_missed_cleavage_2=2
109 msfragger.analyzer_types=all
110 msfragger.calibrate_mass=2
111 msfragger.check_spectral_files=true
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=0/1/2/3
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=0.01
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=1
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,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 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=150
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=--only-psms --no-terminate --post-processing-tdc
207 percolator.keep-tsv-files=false
208 percolator.min-prob=0.5
209 percolator.run-percolator=true
210 phi-report.dont-use-prot-proph-file=false
211 phi-report.filter=--sequential --picked --prot 0.01
212 phi-report.pep-level-summary=false
213 phi-report.print-decoys=false
214 phi-report.prot-level-summary=true
215 phi-report.remove-contaminants=false
216 phi-report.run-report=true
217 protein-prophet.cmd-opts=--maxppmdiff 2000000
218 protein-prophet.run-protein-prophet=true
219 ptmprophet.cmdline=NOSTACK KEEPOLD STATIC FRAGPPMTOL\=10 EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
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=00.2
234 ptmshepherd.diagmine_fragMinFoldChange=3.0
235 ptmshepherd.diagmine_fragMinPropensity=00.1
236 ptmshepherd.diagmine_fragMinSpecDiff=00.1
237 ptmshepherd.diagmine_minIonsPerSpec=2
238 ptmshepherd.diagmine_minPeps=25
239 ptmshepherd.diagmine_pepMinFoldChange=3.0
240 ptmshepherd.diagmine_pepMinSpecDiff=00.2
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=ciRT
313 speclibgen.easypqp.select-file.text=
314 speclibgen.easypqp.select-im-file.text=
315 speclibgen.keep-intermediate-files=false
316 speclibgen.run-speclibgen=false
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.input.data-type.im-ms=false
358 workflow.input.data-type.regular-ms=true
359 workflow.misc.save-sdrf=true
360 workflow.misc.sdrf-type=Default
361 workflow.saved-with-ver=23.0-build14