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comparison workflows/Nonspecific-HLA.workflow @ 0:14785481da2b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
author galaxyp
date Wed, 10 Jul 2024 06:15:00 +0000
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comparison
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-1:000000000000 0:14785481da2b
1 # Workflow: Nonspecific-HLA
2
3 crystalc.run-crystalc=false
4 database.decoy-tag=rev_
5 diann.fragpipe.cmd-opts=
6 diann.heavy=
7 diann.library=
8 diann.light=
9 diann.medium=
10 diann.q-value=0.01
11 diann.quantification-strategy=3
12 diann.run-dia-nn=false
13 diann.run-dia-plex=false
14 diann.run-specific-protein-q-value=false
15 diann.unrelated-runs=false
16 diann.use-predicted-spectra=false
17 diaumpire.AdjustFragIntensity=true
18 diaumpire.BoostComplementaryIon=false
19 diaumpire.CorrThreshold=0
20 diaumpire.DeltaApex=0.2
21 diaumpire.ExportPrecursorPeak=false
22 diaumpire.Q1=true
23 diaumpire.Q2=true
24 diaumpire.Q3=true
25 diaumpire.RFmax=500
26 diaumpire.RPmax=25
27 diaumpire.RTOverlap=0.3
28 diaumpire.SE.EstimateBG=false
29 diaumpire.SE.IsoPattern=0.3
30 diaumpire.SE.MS1PPM=10
31 diaumpire.SE.MS2PPM=20
32 diaumpire.SE.MS2SN=1.1
33 diaumpire.SE.MassDefectFilter=true
34 diaumpire.SE.MassDefectOffset=0.1
35 diaumpire.SE.NoMissedScan=1
36 diaumpire.SE.SN=1.1
37 diaumpire.run-diaumpire=false
38 freequant.mz-tol=10
39 freequant.rt-tol=0.4
40 freequant.run-freequant=false
41 ionquant.excludemods=
42 ionquant.heavy=
43 ionquant.imtol=0.05
44 ionquant.ionfdr=0.01
45 ionquant.light=
46 ionquant.locprob=0.75
47 ionquant.maxlfq=1
48 ionquant.mbr=1
49 ionquant.mbrimtol=0.05
50 ionquant.mbrmincorr=0
51 ionquant.mbrrttol=1
52 ionquant.mbrtoprun=10
53 ionquant.medium=
54 ionquant.minfreq=0
55 ionquant.minions=2
56 ionquant.minisotopes=2
57 ionquant.minscans=3
58 ionquant.mztol=10
59 ionquant.normalization=1
60 ionquant.peptidefdr=1
61 ionquant.proteinfdr=1
62 ionquant.requantify=1
63 ionquant.rttol=0.4
64 ionquant.run-ionquant=true
65 ionquant.tp=0
66 ionquant.uniqueness=0
67 ionquant.use-labeling=false
68 ionquant.use-lfq=true
69 ionquant.writeindex=0
70 msbooster.predict-rt=true
71 msbooster.predict-spectra=true
72 msbooster.run-msbooster=true
73 msbooster.use-correlated-features=false
74 msfragger.Y_type_masses=
75 msfragger.activation_types=all
76 msfragger.add_topN_complementary=0
77 msfragger.allowed_missed_cleavage_1=2
78 msfragger.allowed_missed_cleavage_2=2
79 msfragger.calibrate_mass=2
80 msfragger.check_spectral_files=true
81 msfragger.clip_nTerm_M=true
82 msfragger.deisotope=1
83 msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
84 msfragger.deneutralloss=1
85 msfragger.diagnostic_fragments=
86 msfragger.diagnostic_intensity_filter=0
87 msfragger.digest_max_length=25
88 msfragger.digest_min_length=7
89 msfragger.fragment_ion_series=b,y
90 msfragger.fragment_mass_tolerance=20
91 msfragger.fragment_mass_units=1
92 msfragger.group_variable=0
93 msfragger.intensity_transform=1
94 msfragger.ion_series_definitions=
95 msfragger.isotope_error=0/1
96 msfragger.labile_search_mode=off
97 msfragger.localize_delta_mass=false
98 msfragger.mass_diff_to_variable_mod=0
99 msfragger.mass_offsets=0
100 msfragger.max_fragment_charge=2
101 msfragger.max_variable_mods_combinations=5000
102 msfragger.max_variable_mods_per_peptide=3
103 msfragger.min_fragments_modelling=2
104 msfragger.min_matched_fragments=5
105 msfragger.min_sequence_matches=2
106 msfragger.minimum_peaks=15
107 msfragger.minimum_ratio=0.00
108 msfragger.misc.fragger.clear-mz-hi=0
109 msfragger.misc.fragger.clear-mz-lo=0
110 msfragger.misc.fragger.digest-mass-hi=5000
111 msfragger.misc.fragger.digest-mass-lo=200
112 msfragger.misc.fragger.enzyme-dropdown-1=nonspecific
113 msfragger.misc.fragger.enzyme-dropdown-2=null
114 msfragger.misc.fragger.precursor-charge-hi=4
115 msfragger.misc.fragger.precursor-charge-lo=1
116 msfragger.misc.fragger.remove-precursor-range-hi=1.5
117 msfragger.misc.fragger.remove-precursor-range-lo=-1.5
118 msfragger.misc.slice-db=1
119 msfragger.num_enzyme_termini=0
120 msfragger.output_format=pepXML_pin
121 msfragger.output_max_expect=50
122 msfragger.output_report_topN=1
123 msfragger.output_report_topN_dia1=5
124 msfragger.output_report_topN_dia2=3
125 msfragger.override_charge=false
126 msfragger.precursor_mass_lower=-20
127 msfragger.precursor_mass_mode=selected
128 msfragger.precursor_mass_units=1
129 msfragger.precursor_mass_upper=20
130 msfragger.precursor_true_tolerance=15
131 msfragger.precursor_true_units=1
132 msfragger.remainder_fragment_masses=-18.01056 79.96633
133 msfragger.remove_precursor_peak=1
134 msfragger.report_alternative_proteins=true
135 msfragger.require_precursor=true
136 msfragger.restrict_deltamass_to=all
137 msfragger.reuse_dia_fragment_peaks=false
138 msfragger.run-msfragger=true
139 msfragger.search_enzyme_cut_1=-
140 msfragger.search_enzyme_cut_2=-
141 msfragger.search_enzyme_name_1=nonspecific
142 msfragger.search_enzyme_name_2=null
143 msfragger.search_enzyme_nocut_1=
144 msfragger.search_enzyme_nocut_2=
145 msfragger.search_enzyme_sense_1=C
146 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
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
149 msfragger.track_zero_topN=0
150 msfragger.use_all_mods_in_first_search=false
151 msfragger.use_topN_peaks=300
152 msfragger.write_calibrated_mzml=false
153 msfragger.write_uncalibrated_mgf=false
154 msfragger.zero_bin_accept_expect=0
155 msfragger.zero_bin_mult_expect=1
156 opair.activation1=HCD
157 opair.activation2=ETD
158 opair.filterOxonium=true
159 opair.glyco_db=
160 opair.max_glycans=4
161 opair.max_isotope_error=2
162 opair.min_isotope_error=0
163 opair.ms1_tol=20
164 opair.ms2_tol=20
165 opair.oxonium_filtering_file=
166 opair.oxonium_minimum_intensity=0.05
167 opair.reverse_scan_order=false
168 opair.run-opair=false
169 opair.single_scan_type=false
170 peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
171 peptide-prophet.combine-pepxml=false
172 peptide-prophet.run-peptide-prophet=false
173 percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
174 percolator.keep-tsv-files=false
175 percolator.min-prob=0.5
176 percolator.run-percolator=true
177 phi-report.dont-use-prot-proph-file=false
178 phi-report.filter=--sequential --prot 1
179 phi-report.pep-level-summary=true
180 phi-report.philosoher-msstats=false
181 phi-report.print-decoys=false
182 phi-report.prot-level-summary=true
183 phi-report.remove-contaminants=false
184 phi-report.run-report=true
185 protein-prophet.cmd-opts=--maxppmdiff 2000000
186 protein-prophet.run-protein-prophet=true
187 ptmprophet.cmdline=
188 ptmprophet.run-ptmprophet=false
189 ptmshepherd.adv_params=false
190 ptmshepherd.annotation-common=false
191 ptmshepherd.annotation-custom=false
192 ptmshepherd.annotation-glyco=false
193 ptmshepherd.annotation-unimod=true
194 ptmshepherd.annotation_file=
195 ptmshepherd.annotation_tol=0.01
196 ptmshepherd.cap_y_ions=
197 ptmshepherd.decoy_type=1
198 ptmshepherd.diag_ions=
199 ptmshepherd.diagextract_mode=false
200 ptmshepherd.diagmine_diagMinFoldChange=3.0
201 ptmshepherd.diagmine_diagMinSpecDiff=00.2
202 ptmshepherd.diagmine_fragMinFoldChange=3.0
203 ptmshepherd.diagmine_fragMinPropensity=00.1
204 ptmshepherd.diagmine_fragMinSpecDiff=00.1
205 ptmshepherd.diagmine_minIonsPerSpec=2
206 ptmshepherd.diagmine_minPeps=25
207 ptmshepherd.diagmine_mode=false
208 ptmshepherd.diagmine_pepMinFoldChange=3.0
209 ptmshepherd.diagmine_pepMinSpecDiff=00.2
210 ptmshepherd.glyco_adducts=
211 ptmshepherd.glyco_fdr=1.00
212 ptmshepherd.glyco_isotope_max=3
213 ptmshepherd.glyco_isotope_min=-1
214 ptmshepherd.glyco_mode=false
215 ptmshepherd.glyco_ppm_tol=50
216 ptmshepherd.glycodatabase=
217 ptmshepherd.histo_smoothbins=2
218 ptmshepherd.iontype_a=false
219 ptmshepherd.iontype_b=true
220 ptmshepherd.iontype_c=false
221 ptmshepherd.iontype_x=false
222 ptmshepherd.iontype_y=true
223 ptmshepherd.iontype_z=false
224 ptmshepherd.localization_allowed_res=
225 ptmshepherd.localization_background=4
226 ptmshepherd.max_adducts=0
227 ptmshepherd.n_glyco=true
228 ptmshepherd.normalization-psms=true
229 ptmshepherd.normalization-scans=false
230 ptmshepherd.output_extended=false
231 ptmshepherd.peakpicking_mass_units=0
232 ptmshepherd.peakpicking_minPsm=10
233 ptmshepherd.peakpicking_promRatio=0.3
234 ptmshepherd.peakpicking_width=0.002
235 ptmshepherd.precursor_mass_units=0
236 ptmshepherd.precursor_tol=0.01
237 ptmshepherd.print_decoys=false
238 ptmshepherd.prob_dhexOx=2,0.5,0.1
239 ptmshepherd.prob_dhexY=2,0.5
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=
246 ptmshepherd.remove_glycan_delta_mass=true
247 ptmshepherd.run-shepherd=false
248 ptmshepherd.spectra_maxfragcharge=2
249 ptmshepherd.spectra_ppmtol=20
250 ptmshepherd.varmod_masses=
251 quantitation.run-label-free-quant=false
252 run-psm-validation=true
253 run-validation-tab=true
254 saintexpress.fragpipe.cmd-opts=
255 saintexpress.max-replicates=10
256 saintexpress.run-saint-express=false
257 saintexpress.virtual-controls=100
258 speclibgen.easypqp.extras.max_delta_ppm=15
259 speclibgen.easypqp.extras.max_delta_unimod=0.02
260 speclibgen.easypqp.extras.rt_lowess_fraction=0
261 speclibgen.easypqp.fragment.a=false
262 speclibgen.easypqp.fragment.b=true
263 speclibgen.easypqp.fragment.c=false
264 speclibgen.easypqp.fragment.x=false
265 speclibgen.easypqp.fragment.y=true
266 speclibgen.easypqp.fragment.z=false
267 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
268 speclibgen.easypqp.neutral_loss=false
269 speclibgen.easypqp.rt-cal=noiRT
270 speclibgen.easypqp.select-file.text=
271 speclibgen.easypqp.select-im-file.text=
272 speclibgen.keep-intermediate-files=false
273 speclibgen.run-speclibgen=false
274 tab-run.delete_calibrated_mzml=false
275 tab-run.delete_temp_files=false
276 tab-run.sub_mzml_prob_threshold=0.5
277 tab-run.write_sub_mzml=false
278 tmtintegrator.add_Ref=-1
279 tmtintegrator.aggregation_method=0
280 tmtintegrator.allow_overlabel=true
281 tmtintegrator.allow_unlabeled=true
282 tmtintegrator.best_psm=true
283 tmtintegrator.channel_num=TMT-6
284 tmtintegrator.dont-run-fq-lq=false
285 tmtintegrator.glyco_qval=-1
286 tmtintegrator.groupby=0
287 tmtintegrator.log2transformed=true
288 tmtintegrator.max_pep_prob_thres=0
289 tmtintegrator.min_ntt=0
290 tmtintegrator.min_pep_prob=0.9
291 tmtintegrator.min_percent=0.05
292 tmtintegrator.min_purity=0.5
293 tmtintegrator.min_site_prob=-1
294 tmtintegrator.mod_tag=none
295 tmtintegrator.ms1_int=true
296 tmtintegrator.outlier_removal=true
297 tmtintegrator.print_RefInt=false
298 tmtintegrator.prot_exclude=none
299 tmtintegrator.prot_norm=0
300 tmtintegrator.psm_norm=false
301 tmtintegrator.quant_level=2
302 tmtintegrator.ref_tag=Bridge
303 tmtintegrator.run-tmtintegrator=false
304 tmtintegrator.tolerance=20
305 tmtintegrator.top3_pep=true
306 tmtintegrator.unique_gene=0
307 tmtintegrator.unique_pep=false
308 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>
310 workflow.input.data-type.im-ms=false
311 workflow.input.data-type.regular-ms=true
312 workflow.saved-with-ver=20.0-build5