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comparison workflows/Nonspecific-HLA.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
parents 41990c43f371
children
comparison
equal deleted inserted replaced
6:59fec1e2a6c3 7:b4f6df8fa89b
1 # Workflow: Nonspecific-HLA 1 # Workflow: Nonspecific-HLA
2 2
3 crystalc.run-crystalc=false 3 crystalc.run-crystalc=false
4 database.decoy-tag=rev_ 4 database.decoy-tag=rev_
5 diann.fragpipe.cmd-opts= 5 diann.channel-normalization-strategy=0
6 diann.cmd-opts=
7 diann.generate-msstats=true
6 diann.heavy= 8 diann.heavy=
7 diann.library= 9 diann.library=
8 diann.light= 10 diann.light=
9 diann.medium= 11 diann.medium=
12 diann.min-site-prob=0.75
13 diann.mod-tag=
10 diann.q-value=0.01 14 diann.q-value=0.01
11 diann.quantification-strategy=3 15 diann.quantification-strategy=3
16 diann.quantification-strategy-2=2
12 diann.run-dia-nn=false 17 diann.run-dia-nn=false
13 diann.run-dia-plex=false 18 diann.run-dia-plex=false
14 diann.run-specific-protein-q-value=false 19 diann.run-specific-protein-q-value=false
15 diann.unrelated-runs=false 20 diann.unrelated-runs=false
16 diann.use-predicted-spectra=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
17 diaumpire.AdjustFragIntensity=true 30 diaumpire.AdjustFragIntensity=true
18 diaumpire.BoostComplementaryIon=false 31 diaumpire.BoostComplementaryIon=false
19 diaumpire.CorrThreshold=0 32 diaumpire.CorrThreshold=0
20 diaumpire.DeltaApex=0.2 33 diaumpire.DeltaApex=0.2
21 diaumpire.ExportPrecursorPeak=false 34 diaumpire.ExportPrecursorPeak=false
33 diaumpire.SE.MassDefectFilter=true 46 diaumpire.SE.MassDefectFilter=true
34 diaumpire.SE.MassDefectOffset=0.1 47 diaumpire.SE.MassDefectOffset=0.1
35 diaumpire.SE.NoMissedScan=1 48 diaumpire.SE.NoMissedScan=1
36 diaumpire.SE.SN=1.1 49 diaumpire.SE.SN=1.1
37 diaumpire.run-diaumpire=false 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
38 freequant.mz-tol=10 59 freequant.mz-tol=10
39 freequant.rt-tol=0.4 60 freequant.rt-tol=0.4
40 freequant.run-freequant=false 61 freequant.run-freequant=false
41 ionquant.excludemods= 62 ionquant.excludemods=
63 ionquant.formula=
42 ionquant.heavy= 64 ionquant.heavy=
43 ionquant.imtol=0.05 65 ionquant.imtol=0.05
44 ionquant.ionfdr=0.01 66 ionquant.ionfdr=0.01
45 ionquant.light= 67 ionquant.light=
46 ionquant.locprob=0.75 68 ionquant.locprob=0.75
50 ionquant.mbrmincorr=0 72 ionquant.mbrmincorr=0
51 ionquant.mbrrttol=1 73 ionquant.mbrrttol=1
52 ionquant.mbrtoprun=10 74 ionquant.mbrtoprun=10
53 ionquant.medium= 75 ionquant.medium=
54 ionquant.minfreq=0 76 ionquant.minfreq=0
55 ionquant.minions=2 77 ionquant.minions=1
56 ionquant.minisotopes=2 78 ionquant.minisotopes=2
57 ionquant.minscans=3 79 ionquant.minscans=3
58 ionquant.mztol=10 80 ionquant.mztol=10
59 ionquant.normalization=1 81 ionquant.normalization=1
60 ionquant.peptidefdr=1 82 ionquant.peptidefdr=1
65 ionquant.tp=0 87 ionquant.tp=0
66 ionquant.uniqueness=0 88 ionquant.uniqueness=0
67 ionquant.use-labeling=false 89 ionquant.use-labeling=false
68 ionquant.use-lfq=true 90 ionquant.use-lfq=true
69 ionquant.writeindex=0 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
70 msbooster.predict-rt=true 99 msbooster.predict-rt=true
71 msbooster.predict-spectra=true 100 msbooster.predict-spectra=true
101 msbooster.rt-model=DIA-NN
72 msbooster.run-msbooster=true 102 msbooster.run-msbooster=true
73 msbooster.use-correlated-features=false 103 msbooster.spectra-model=DIA-NN
104 msbooster.spectral-library-path=
74 msfragger.Y_type_masses= 105 msfragger.Y_type_masses=
75 msfragger.activation_types=all 106 msfragger.activation_types=all
76 msfragger.add_topN_complementary=0
77 msfragger.allowed_missed_cleavage_1=2 107 msfragger.allowed_missed_cleavage_1=2
78 msfragger.allowed_missed_cleavage_2=2 108 msfragger.allowed_missed_cleavage_2=2
109 msfragger.analyzer_types=all
79 msfragger.calibrate_mass=2 110 msfragger.calibrate_mass=2
80 msfragger.check_spectral_files=true 111 msfragger.check_spectral_files=true
81 msfragger.clip_nTerm_M=true 112 msfragger.clip_nTerm_M=true
82 msfragger.deisotope=1 113 msfragger.deisotope=1
83 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) 114 msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
95 msfragger.isotope_error=0/1 126 msfragger.isotope_error=0/1
96 msfragger.labile_search_mode=off 127 msfragger.labile_search_mode=off
97 msfragger.localize_delta_mass=false 128 msfragger.localize_delta_mass=false
98 msfragger.mass_diff_to_variable_mod=0 129 msfragger.mass_diff_to_variable_mod=0
99 msfragger.mass_offsets=0 130 msfragger.mass_offsets=0
131 msfragger.mass_offsets_detailed=
100 msfragger.max_fragment_charge=2 132 msfragger.max_fragment_charge=2
101 msfragger.max_variable_mods_combinations=5000 133 msfragger.max_variable_mods_combinations=5000
102 msfragger.max_variable_mods_per_peptide=3 134 msfragger.max_variable_mods_per_peptide=3
103 msfragger.min_fragments_modelling=2 135 msfragger.min_fragments_modelling=2
104 msfragger.min_matched_fragments=5 136 msfragger.min_matched_fragments=5
118 msfragger.misc.slice-db=1 150 msfragger.misc.slice-db=1
119 msfragger.num_enzyme_termini=0 151 msfragger.num_enzyme_termini=0
120 msfragger.output_format=pepXML_pin 152 msfragger.output_format=pepXML_pin
121 msfragger.output_max_expect=50 153 msfragger.output_max_expect=50
122 msfragger.output_report_topN=1 154 msfragger.output_report_topN=1
155 msfragger.output_report_topN_dda_plus=5
123 msfragger.output_report_topN_dia1=5 156 msfragger.output_report_topN_dia1=5
124 msfragger.output_report_topN_dia2=3
125 msfragger.override_charge=false 157 msfragger.override_charge=false
126 msfragger.precursor_mass_lower=-20 158 msfragger.precursor_mass_lower=-20
127 msfragger.precursor_mass_mode=selected 159 msfragger.precursor_mass_mode=selected
128 msfragger.precursor_mass_units=1 160 msfragger.precursor_mass_units=1
129 msfragger.precursor_mass_upper=20 161 msfragger.precursor_mass_upper=20
134 msfragger.report_alternative_proteins=true 166 msfragger.report_alternative_proteins=true
135 msfragger.require_precursor=true 167 msfragger.require_precursor=true
136 msfragger.restrict_deltamass_to=all 168 msfragger.restrict_deltamass_to=all
137 msfragger.reuse_dia_fragment_peaks=false 169 msfragger.reuse_dia_fragment_peaks=false
138 msfragger.run-msfragger=true 170 msfragger.run-msfragger=true
139 msfragger.search_enzyme_cut_1=- 171 msfragger.search_enzyme_cut_1=@
140 msfragger.search_enzyme_cut_2=- 172 msfragger.search_enzyme_cut_2=@
141 msfragger.search_enzyme_name_1=nonspecific 173 msfragger.search_enzyme_name_1=nonspecific
142 msfragger.search_enzyme_name_2=null 174 msfragger.search_enzyme_name_2=null
143 msfragger.search_enzyme_nocut_1= 175 msfragger.search_enzyme_nocut_1=
144 msfragger.search_enzyme_nocut_2= 176 msfragger.search_enzyme_nocut_2=
145 msfragger.search_enzyme_sense_1=C 177 msfragger.search_enzyme_sense_1=C
146 msfragger.search_enzyme_sense_2=C 178 msfragger.search_enzyme_sense_2=C
147 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),false,-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,-1 179 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),false,-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
148 msfragger.table.var-mods=15.9949,M,true,2; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQ,true,1; -18.0106,nE,true,1; 119.0041,C,true,1; 0.98402,N,false,1; 8.014199,K,false,1; 10.008269,R,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,1 180 msfragger.table.var-mods=15.9949,M,true,2; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQ,true,1; -18.0106,nE,true,1; 119.0041,C,true,1; 0.98402,N,false,1; 8.014199,K,false,1; 10.008269,R,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
149 msfragger.track_zero_topN=0 181 msfragger.track_zero_topN=0
150 msfragger.use_all_mods_in_first_search=false 182 msfragger.use_all_mods_in_first_search=false
183 msfragger.use_detailed_offsets=false
151 msfragger.use_topN_peaks=300 184 msfragger.use_topN_peaks=300
152 msfragger.write_calibrated_mzml=false 185 msfragger.write_calibrated_mzml=false
153 msfragger.write_uncalibrated_mgf=false
154 msfragger.zero_bin_accept_expect=0 186 msfragger.zero_bin_accept_expect=0
155 msfragger.zero_bin_mult_expect=1 187 msfragger.zero_bin_mult_expect=1
156 opair.activation1=HCD 188 opair.activation1=HCD
157 opair.activation2=ETD 189 opair.activation2=ETD
190 opair.allowed_sites=
158 opair.filterOxonium=true 191 opair.filterOxonium=true
159 opair.glyco_db= 192 opair.glyco_db=
160 opair.max_glycans=4 193 opair.max_glycans=4
161 opair.max_isotope_error=2 194 opair.max_isotope_error=2
162 opair.min_isotope_error=0 195 opair.min_isotope_error=0
175 percolator.min-prob=0.5 208 percolator.min-prob=0.5
176 percolator.run-percolator=true 209 percolator.run-percolator=true
177 phi-report.dont-use-prot-proph-file=false 210 phi-report.dont-use-prot-proph-file=false
178 phi-report.filter=--sequential --prot 1 211 phi-report.filter=--sequential --prot 1
179 phi-report.pep-level-summary=true 212 phi-report.pep-level-summary=true
180 phi-report.philosoher-msstats=false
181 phi-report.print-decoys=false 213 phi-report.print-decoys=false
182 phi-report.prot-level-summary=true 214 phi-report.prot-level-summary=true
183 phi-report.remove-contaminants=false 215 phi-report.remove-contaminants=false
184 phi-report.run-report=true 216 phi-report.run-report=true
185 protein-prophet.cmd-opts=--maxppmdiff 2000000 217 protein-prophet.cmd-opts=--maxppmdiff 2000000
186 protein-prophet.run-protein-prophet=true 218 protein-prophet.run-protein-prophet=true
187 ptmprophet.cmdline= 219 ptmprophet.cmdline=
220 ptmprophet.override-defaults=false
188 ptmprophet.run-ptmprophet=false 221 ptmprophet.run-ptmprophet=false
189 ptmshepherd.adv_params=false 222 ptmshepherd.adv_params=false
190 ptmshepherd.annotation-common=false 223 ptmshepherd.annotation-common=false
191 ptmshepherd.annotation-custom=false 224 ptmshepherd.annotation-custom=false
192 ptmshepherd.annotation-glyco=false 225 ptmshepherd.annotation-glyco=false
194 ptmshepherd.annotation_file= 227 ptmshepherd.annotation_file=
195 ptmshepherd.annotation_tol=0.01 228 ptmshepherd.annotation_tol=0.01
196 ptmshepherd.cap_y_ions= 229 ptmshepherd.cap_y_ions=
197 ptmshepherd.decoy_type=1 230 ptmshepherd.decoy_type=1
198 ptmshepherd.diag_ions= 231 ptmshepherd.diag_ions=
199 ptmshepherd.diagextract_mode=false
200 ptmshepherd.diagmine_diagMinFoldChange=3.0 232 ptmshepherd.diagmine_diagMinFoldChange=3.0
201 ptmshepherd.diagmine_diagMinSpecDiff=00.2 233 ptmshepherd.diagmine_diagMinSpecDiff=00.2
202 ptmshepherd.diagmine_fragMinFoldChange=3.0 234 ptmshepherd.diagmine_fragMinFoldChange=3.0
203 ptmshepherd.diagmine_fragMinPropensity=00.1 235 ptmshepherd.diagmine_fragMinPropensity=00.1
204 ptmshepherd.diagmine_fragMinSpecDiff=00.1 236 ptmshepherd.diagmine_fragMinSpecDiff=00.1
205 ptmshepherd.diagmine_minIonsPerSpec=2 237 ptmshepherd.diagmine_minIonsPerSpec=2
206 ptmshepherd.diagmine_minPeps=25 238 ptmshepherd.diagmine_minPeps=25
207 ptmshepherd.diagmine_mode=false
208 ptmshepherd.diagmine_pepMinFoldChange=3.0 239 ptmshepherd.diagmine_pepMinFoldChange=3.0
209 ptmshepherd.diagmine_pepMinSpecDiff=00.2 240 ptmshepherd.diagmine_pepMinSpecDiff=00.2
210 ptmshepherd.glyco_adducts=
211 ptmshepherd.glyco_fdr=1.00 241 ptmshepherd.glyco_fdr=1.00
212 ptmshepherd.glyco_isotope_max=3 242 ptmshepherd.glyco_isotope_max=3
213 ptmshepherd.glyco_isotope_min=-1 243 ptmshepherd.glyco_isotope_min=-1
214 ptmshepherd.glyco_mode=false
215 ptmshepherd.glyco_ppm_tol=50 244 ptmshepherd.glyco_ppm_tol=50
216 ptmshepherd.glycodatabase= 245 ptmshepherd.glycodatabase=
217 ptmshepherd.histo_smoothbins=2 246 ptmshepherd.histo_smoothbins=2
218 ptmshepherd.iontype_a=false 247 ptmshepherd.iontype_a=false
219 ptmshepherd.iontype_b=true 248 ptmshepherd.iontype_b=true
220 ptmshepherd.iontype_c=false 249 ptmshepherd.iontype_c=false
221 ptmshepherd.iontype_x=false 250 ptmshepherd.iontype_x=false
222 ptmshepherd.iontype_y=true 251 ptmshepherd.iontype_y=true
223 ptmshepherd.iontype_z=false 252 ptmshepherd.iontype_z=false
253 ptmshepherd.iterloc_maxEpoch=100
254 ptmshepherd.iterloc_mode=false
224 ptmshepherd.localization_allowed_res= 255 ptmshepherd.localization_allowed_res=
225 ptmshepherd.localization_background=4
226 ptmshepherd.max_adducts=0
227 ptmshepherd.n_glyco=true 256 ptmshepherd.n_glyco=true
228 ptmshepherd.normalization-psms=true 257 ptmshepherd.normalization-psms=true
229 ptmshepherd.normalization-scans=false 258 ptmshepherd.normalization-scans=false
230 ptmshepherd.output_extended=false 259 ptmshepherd.output_extended=false
231 ptmshepherd.peakpicking_mass_units=0 260 ptmshepherd.peakpicking_mass_units=0
233 ptmshepherd.peakpicking_promRatio=0.3 262 ptmshepherd.peakpicking_promRatio=0.3
234 ptmshepherd.peakpicking_width=0.002 263 ptmshepherd.peakpicking_width=0.002
235 ptmshepherd.precursor_mass_units=0 264 ptmshepherd.precursor_mass_units=0
236 ptmshepherd.precursor_tol=0.01 265 ptmshepherd.precursor_tol=0.01
237 ptmshepherd.print_decoys=false 266 ptmshepherd.print_decoys=false
238 ptmshepherd.prob_dhexOx=2,0.5,0.1 267 ptmshepherd.print_full_glyco_params=false
239 ptmshepherd.prob_dhexY=2,0.5 268 ptmshepherd.prob_mass=0.5
240 ptmshepherd.prob_neuacOx=2,0.05,0.2
241 ptmshepherd.prob_neugcOx=2,0.05,0.2
242 ptmshepherd.prob_phosphoOx=2,0.05,0.2
243 ptmshepherd.prob_regY=5,0.5
244 ptmshepherd.prob_sulfoOx=2,0.05,0.2
245 ptmshepherd.remainder_masses= 269 ptmshepherd.remainder_masses=
246 ptmshepherd.remove_glycan_delta_mass=true 270 ptmshepherd.remove_glycan_delta_mass=true
247 ptmshepherd.run-shepherd=false 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
248 ptmshepherd.spectra_maxfragcharge=2 278 ptmshepherd.spectra_maxfragcharge=2
249 ptmshepherd.spectra_ppmtol=20 279 ptmshepherd.spectra_ppmtol=20
250 ptmshepherd.varmod_masses= 280 ptmshepherd.varmod_masses=
251 quantitation.run-label-free-quant=false 281 quantitation.run-label-free-quant=false
252 run-psm-validation=true 282 run-psm-validation=true
253 run-validation-tab=true 283 run-validation-tab=true
254 saintexpress.fragpipe.cmd-opts= 284 saintexpress.cmd-opts=
255 saintexpress.max-replicates=10 285 saintexpress.max-replicates=10
256 saintexpress.run-saint-express=false 286 saintexpress.run-saint-express=false
257 saintexpress.virtual-controls=100 287 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
258 speclibgen.easypqp.extras.max_delta_ppm=15 299 speclibgen.easypqp.extras.max_delta_ppm=15
259 speclibgen.easypqp.extras.max_delta_unimod=0.02 300 speclibgen.easypqp.extras.max_delta_unimod=0.02
301 speclibgen.easypqp.extras.max_glycan_qval=1
260 speclibgen.easypqp.extras.rt_lowess_fraction=0 302 speclibgen.easypqp.extras.rt_lowess_fraction=0
261 speclibgen.easypqp.fragment.a=false 303 speclibgen.easypqp.fragment.a=false
262 speclibgen.easypqp.fragment.b=true 304 speclibgen.easypqp.fragment.b=true
263 speclibgen.easypqp.fragment.c=false 305 speclibgen.easypqp.fragment.c=false
264 speclibgen.easypqp.fragment.x=false 306 speclibgen.easypqp.fragment.x=false
265 speclibgen.easypqp.fragment.y=true 307 speclibgen.easypqp.fragment.y=true
266 speclibgen.easypqp.fragment.z=false 308 speclibgen.easypqp.fragment.z=false
267 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM 309 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
310 speclibgen.easypqp.labile_mode=Regular (not glyco)
268 speclibgen.easypqp.neutral_loss=false 311 speclibgen.easypqp.neutral_loss=false
269 speclibgen.easypqp.rt-cal=noiRT 312 speclibgen.easypqp.rt-cal=noiRT
270 speclibgen.easypqp.select-file.text= 313 speclibgen.easypqp.select-file.text=
271 speclibgen.easypqp.select-im-file.text= 314 speclibgen.easypqp.select-im-file.text=
272 speclibgen.keep-intermediate-files=false 315 speclibgen.keep-intermediate-files=false
273 speclibgen.run-speclibgen=false 316 speclibgen.run-speclibgen=false
274 tab-run.delete_calibrated_mzml=false 317 tab-run.delete_calibrated_mzml=false
275 tab-run.delete_temp_files=false 318 tab-run.delete_temp_files=false
319 tab-run.export_matched_fragments=false
276 tab-run.sub_mzml_prob_threshold=0.5 320 tab-run.sub_mzml_prob_threshold=0.5
277 tab-run.write_sub_mzml=false 321 tab-run.write_sub_mzml=false
278 tmtintegrator.add_Ref=-1 322 tmtintegrator.add_Ref=-1
279 tmtintegrator.aggregation_method=0 323 tmtintegrator.aggregation_method=0
280 tmtintegrator.allow_overlabel=true 324 tmtintegrator.allow_overlabel=true
281 tmtintegrator.allow_unlabeled=true 325 tmtintegrator.allow_unlabeled=true
282 tmtintegrator.best_psm=true 326 tmtintegrator.best_psm=true
283 tmtintegrator.channel_num=TMT-6 327 tmtintegrator.channel_num=TMT-6
284 tmtintegrator.dont-run-fq-lq=false 328 tmtintegrator.extraction_tool=IonQuant
285 tmtintegrator.glyco_qval=-1 329 tmtintegrator.glyco_qval=-1
286 tmtintegrator.groupby=0 330 tmtintegrator.groupby=-1
287 tmtintegrator.log2transformed=true 331 tmtintegrator.log2transformed=true
288 tmtintegrator.max_pep_prob_thres=0 332 tmtintegrator.max_pep_prob_thres=0
289 tmtintegrator.min_ntt=0 333 tmtintegrator.min_ntt=0
290 tmtintegrator.min_pep_prob=0.9 334 tmtintegrator.min_pep_prob=0.9
291 tmtintegrator.min_percent=0.05 335 tmtintegrator.min_percent=0.05
292 tmtintegrator.min_purity=0.5 336 tmtintegrator.min_purity=0.5
337 tmtintegrator.min_resolution=0
293 tmtintegrator.min_site_prob=-1 338 tmtintegrator.min_site_prob=-1
339 tmtintegrator.min_snr=0
294 tmtintegrator.mod_tag=none 340 tmtintegrator.mod_tag=none
295 tmtintegrator.ms1_int=true 341 tmtintegrator.ms1_int=true
296 tmtintegrator.outlier_removal=true 342 tmtintegrator.outlier_removal=true
343 tmtintegrator.philosopher-msstats=false
297 tmtintegrator.print_RefInt=false 344 tmtintegrator.print_RefInt=false
298 tmtintegrator.prot_exclude=none 345 tmtintegrator.prot_exclude=none
299 tmtintegrator.prot_norm=0 346 tmtintegrator.prot_norm=0
300 tmtintegrator.psm_norm=false 347 tmtintegrator.psm_norm=false
301 tmtintegrator.quant_level=2 348 tmtintegrator.quant_level=2
349 tmtintegrator.ref_d_tag=Pool
302 tmtintegrator.ref_tag=Bridge 350 tmtintegrator.ref_tag=Bridge
303 tmtintegrator.run-tmtintegrator=false 351 tmtintegrator.run-tmtintegrator=false
304 tmtintegrator.tolerance=20 352 tmtintegrator.tolerance=20
305 tmtintegrator.top3_pep=true 353 tmtintegrator.top3_pep=true
306 tmtintegrator.unique_gene=0 354 tmtintegrator.unique_gene=0
307 tmtintegrator.unique_pep=false 355 tmtintegrator.unique_pep=false
308 tmtintegrator.use_glycan_composition=false 356 tmtintegrator.use_glycan_composition=false
309 workflow.description=<p style\="margin-top\: 0in">Nonspecific search, with recommended settings for HLA peptides. Peptide length 7-25. MSFragger search assumes cysteines were not alkylated (i.e. samples were not treated with iodoacetamide). Cysteinylation (C+119) is specified as variable modification. MSFragger rescoring with MSBooster. PSM validation with Percolator. Protein FDR filter is not applied, so each output file (PSM, ion, peptide) is filtered to 1% FDR at that level. If needed, extend to add label-free quantifcation (using IonQuant) or spectral library building with EasyPQP.</p> 357 workflow.description=<p style\="margin-top\: 0in">Nonspecific search, with recommended settings for HLA peptides. Peptide length 7-25. MSFragger search assumes cysteines were not alkylated (i.e. samples were not treated with iodoacetamide). Cysteinylation (C+119) is specified as variable modification. MSFragger rescoring with MSBooster. PSM validation with Percolator. Protein FDR filter is not applied, so each output file (PSM, ion, peptide) is filtered to 1% FDR at that level. If needed, extend to add label-free quantifcation (using IonQuant) or spectral library building with EasyPQP.</p>
310 workflow.input.data-type.im-ms=false 358 workflow.input.data-type.im-ms=false
311 workflow.input.data-type.regular-ms=true 359 workflow.input.data-type.regular-ms=true
312 workflow.saved-with-ver=20.0-build5 360 workflow.misc.save-sdrf=true
361 workflow.misc.sdrf-type=Default
362 workflow.saved-with-ver=23.0-build14