Final edits for release.

tools/fragpipe/.shed.yml

@@ -0,0 +1,11 @@
+owner: galaxyp
+name: fragpipe
+categories:
+- Proteomics
+description: Data analysis for mass spectrometry-based proteomics.
+homepage_url: https://fragpipe.nesvilab.org/
+long_description: |
+  FragPipe is a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data.
+  FragPipe uses MSFragger - an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification.
+remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe
+type: unrestricted

tools/fragpipe/genericize_db.py

@@ -0,0 +1,18 @@
+#!/usr/bin/env python3
+#
+# Prefixes sequence headers in the input FASTA file that are not formatted according to the UniProt, NCBI, or ENSEMBL formats with '>generic|' to avoid being misinterpreted by Philosopher.
+#
+
+import re
+import sys
+
+input_db_file = sys.argv[1]
+output_db_file = sys.argv[2]
+
+with open(input_db_file) as f:
+    input_db = f.readlines()
+
+subbed_lines = [re.sub(r'^>(?!sp\||tr\||db\||AP_|NP_|YP_|XP_|WP_|ENSP|UniRef|nxp|generic)', '>generic|', l) for l in input_db]
+
+with open(output_db_file, 'w') as f:
+    f.writelines(subbed_lines)

tools/fragpipe/test-data/default/outputs/workflow.txt

@@ -0,0 +1,308 @@
+database.decoy-tag=rev_
+diann.fragpipe.cmd-opts=
+diann.heavy=
+diann.library=
+diann.light=
+diann.medium=
+diann.q-value=0.01
+diann.quantification-strategy=3
+diann.run-dia-nn=false
+diann.run-dia-plex=false
+diann.run-specific-protein-q-value=false
+diann.unrelated-runs=false
+diann.use-predicted-spectra=true
+diaumpire.AdjustFragIntensity=true
+diaumpire.BoostComplementaryIon=false
+diaumpire.CorrThreshold=0
+diaumpire.DeltaApex=0.2
+diaumpire.ExportPrecursorPeak=false
+diaumpire.Q1=true
+diaumpire.Q2=true
+diaumpire.Q3=true
+diaumpire.RFmax=500
+diaumpire.RPmax=25
+diaumpire.RTOverlap=0.3
+diaumpire.SE.EstimateBG=false
+diaumpire.SE.IsoPattern=0.3
+diaumpire.SE.MS1PPM=10
+diaumpire.SE.MS2PPM=20
+diaumpire.SE.MS2SN=1.1
+diaumpire.SE.MassDefectFilter=true
+diaumpire.SE.MassDefectOffset=0.1
+diaumpire.SE.NoMissedScan=1
+diaumpire.SE.SN=1.1
+diaumpire.run-diaumpire=false
+freequant.mz-tol=10
+freequant.rt-tol=0.4
+freequant.run-freequant=false
+ionquant.excludemods=
+ionquant.heavy=
+ionquant.imtol=0.05
+ionquant.ionfdr=0.01
+ionquant.light=
+ionquant.locprob=0.75
+ionquant.maxlfq=1
+ionquant.mbr=1
+ionquant.mbrimtol=0.05
+ionquant.mbrmincorr=0
+ionquant.mbrrttol=1
+ionquant.mbrtoprun=10
+ionquant.medium=
+ionquant.minfreq=0
+ionquant.minions=2
+ionquant.minisotopes=2
+ionquant.minscans=3
+ionquant.mztol=10
+ionquant.normalization=1
+ionquant.peptidefdr=1
+ionquant.proteinfdr=1
+ionquant.requantify=1
+ionquant.rttol=0.4
+ionquant.run-ionquant=true
+ionquant.tp=0
+ionquant.uniqueness=0
+ionquant.use-labeling=false
+ionquant.use-lfq=true
+ionquant.writeindex=0
+msbooster.predict-rt=true
+msbooster.predict-spectra=true
+msbooster.run-msbooster=false
+msbooster.use-correlated-features=false
+msfragger.Y_type_masses=
+msfragger.activation_types=all
+msfragger.add_topN_complementary=0
+msfragger.allowed_missed_cleavage_1=2
+msfragger.allowed_missed_cleavage_2=2
+msfragger.calibrate_mass=2
+msfragger.check_spectral_files=true
+msfragger.clip_nTerm_M=true
+msfragger.deisotope=1
+msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
+msfragger.deneutralloss=1
+msfragger.diagnostic_fragments=
+msfragger.diagnostic_intensity_filter=0
+msfragger.digest_max_length=50
+msfragger.digest_min_length=7
+msfragger.fragment_ion_series=b,y
+msfragger.fragment_mass_tolerance=20
+msfragger.fragment_mass_units=1
+msfragger.group_variable=0
+msfragger.intensity_transform=0
+msfragger.ion_series_definitions=
+msfragger.isotope_error=0/1/2/3
+msfragger.labile_search_mode=off
+msfragger.localize_delta_mass=false
+msfragger.mass_diff_to_variable_mod=0
+msfragger.mass_offsets=0
+msfragger.max_fragment_charge=2
+msfragger.max_variable_mods_combinations=5000
+msfragger.max_variable_mods_per_peptide=3
+msfragger.min_fragments_modelling=2
+msfragger.min_matched_fragments=4
+msfragger.min_sequence_matches=2
+msfragger.minimum_peaks=15
+msfragger.minimum_ratio=0.01
+msfragger.misc.fragger.clear-mz-hi=0.0
+msfragger.misc.fragger.clear-mz-lo=0.0
+msfragger.misc.fragger.digest-mass-hi=5000
+msfragger.misc.fragger.digest-mass-lo=500
+msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
+msfragger.misc.fragger.enzyme-dropdown-2=null
+msfragger.misc.fragger.precursor-charge-hi=4
+msfragger.misc.fragger.precursor-charge-lo=1
+msfragger.misc.fragger.remove-precursor-range-hi=1.5
+msfragger.misc.fragger.remove-precursor-range-lo=-1.5
+msfragger.misc.slice-db=1
+msfragger.num_enzyme_termini=2
+msfragger.output_format=pepXML_pin
+msfragger.output_max_expect=50.0
+msfragger.output_report_topN=1
+msfragger.output_report_topN_dia1=5
+msfragger.output_report_topN_dia2=3
+msfragger.override_charge=false
+msfragger.precursor_mass_lower=-20
+msfragger.precursor_mass_mode=selected
+msfragger.precursor_mass_units=1
+msfragger.precursor_mass_upper=20
+msfragger.precursor_true_tolerance=20
+msfragger.precursor_true_units=1
+msfragger.remainder_fragment_masses=
+msfragger.remove_precursor_peak=1
+msfragger.report_alternative_proteins=true
+msfragger.require_precursor=true
+msfragger.restrict_deltamass_to=all
+msfragger.reuse_dia_fragment_peaks=false
+msfragger.run-msfragger=true
+msfragger.search_enzyme_cut_1=KR
+msfragger.search_enzyme_cut_2=
+msfragger.search_enzyme_name_1=stricttrypsin
+msfragger.search_enzyme_name_2=null
+msfragger.search_enzyme_nocut_1=
+msfragger.search_enzyme_nocut_2=
+msfragger.search_enzyme_sense_1=C
+msfragger.search_enzyme_sense_2=C
+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
+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
+msfragger.track_zero_topN=0
+msfragger.use_all_mods_in_first_search=false
+msfragger.use_topN_peaks=150
+msfragger.write_calibrated_mzml=false
+msfragger.write_uncalibrated_mgf=false
+msfragger.zero_bin_accept_expect=0
+msfragger.zero_bin_mult_expect=1
+opair.activation1=HCD
+opair.activation2=ETD
+opair.filterOxonium=true
+opair.glyco_db=
+opair.max_glycans=4
+opair.max_isotope_error=2
+opair.min_isotope_error=0
+opair.ms1_tol=20
+opair.ms2_tol=20
+opair.oxonium_filtering_file=
+opair.oxonium_minimum_intensity=0.05
+opair.reverse_scan_order=false
+opair.run-opair=false
+opair.single_scan_type=false
+peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
+peptide-prophet.combine-pepxml=false
+peptide-prophet.run-peptide-prophet=false
+percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
+percolator.keep-tsv-files=false
+percolator.min-prob=0.5
+percolator.run-percolator=true
+phi-report.dont-use-prot-proph-file=false
+phi-report.filter=--sequential --picked --prot 0.01
+phi-report.pep-level-summary=false
+phi-report.philosoher-msstats=false
+phi-report.print-decoys=false
+phi-report.prot-level-summary=true
+phi-report.remove-contaminants=false
+phi-report.run-report=true
+protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.05
+protein-prophet.run-protein-prophet=true
+ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
+ptmprophet.run-ptmprophet=false
+ptmshepherd.adv_params=false
+ptmshepherd.annotation-common=false
+ptmshepherd.annotation-custom=false
+ptmshepherd.annotation-glyco=false
+ptmshepherd.annotation-unimod=true
+ptmshepherd.annotation_file=
+ptmshepherd.annotation_tol=0.01
+ptmshepherd.cap_y_ions=
+ptmshepherd.decoy_type=1
+ptmshepherd.diag_ions=
+ptmshepherd.diagextract_mode=false
+ptmshepherd.diagmine_diagMinFoldChange=3.0
+ptmshepherd.diagmine_diagMinSpecDiff=00.2
+ptmshepherd.diagmine_fragMinFoldChange=3.0
+ptmshepherd.diagmine_fragMinPropensity=00.1
+ptmshepherd.diagmine_fragMinSpecDiff=00.1
+ptmshepherd.diagmine_minIonsPerSpec=2
+ptmshepherd.diagmine_minPeps=25
+ptmshepherd.diagmine_mode=false
+ptmshepherd.diagmine_pepMinFoldChange=3.0
+ptmshepherd.diagmine_pepMinSpecDiff=00.2
+ptmshepherd.glyco_adducts=
+ptmshepherd.glyco_fdr=1.00
+ptmshepherd.glyco_isotope_max=3
+ptmshepherd.glyco_isotope_min=-1
+ptmshepherd.glyco_mode=false
+ptmshepherd.glyco_ppm_tol=50
+ptmshepherd.glycodatabase=
+ptmshepherd.histo_smoothbins=2
+ptmshepherd.iontype_a=false
+ptmshepherd.iontype_b=true
+ptmshepherd.iontype_c=true
+ptmshepherd.iontype_x=false
+ptmshepherd.iontype_y=true
+ptmshepherd.iontype_z=true
+ptmshepherd.localization_allowed_res=
+ptmshepherd.localization_background=4
+ptmshepherd.max_adducts=0
+ptmshepherd.n_glyco=true
+ptmshepherd.normalization-psms=true
+ptmshepherd.normalization-scans=false
+ptmshepherd.output_extended=false
+ptmshepherd.peakpicking_mass_units=0
+ptmshepherd.peakpicking_minPsm=10
+ptmshepherd.peakpicking_promRatio=0.3
+ptmshepherd.peakpicking_width=0.002
+ptmshepherd.precursor_mass_units=0
+ptmshepherd.precursor_tol=0.01
+ptmshepherd.print_decoys=false
+ptmshepherd.prob_dhexOx=2,0.5,0.1
+ptmshepherd.prob_dhexY=2,0.5
+ptmshepherd.prob_neuacOx=2,0.05,0.2
+ptmshepherd.prob_neugcOx=2,0.05,0.2
+ptmshepherd.prob_phosphoOx=2,0.05,0.2
+ptmshepherd.prob_regY=5,0.5
+ptmshepherd.prob_sulfoOx=2,0.05,0.2
+ptmshepherd.remainder_masses=
+ptmshepherd.remove_glycan_delta_mass=true
+ptmshepherd.run-shepherd=false
+ptmshepherd.spectra_maxfragcharge=2
+ptmshepherd.spectra_ppmtol=20
+ptmshepherd.varmod_masses=
+quantitation.run-label-free-quant=false
+run-psm-validation=true
+run-validation-tab=true
+saintexpress.fragpipe.cmd-opts=
+saintexpress.max-replicates=10
+saintexpress.run-saint-express=false
+saintexpress.virtual-controls=100
+speclibgen.easypqp.extras.max_delta_ppm=15
+speclibgen.easypqp.extras.max_delta_unimod=0.02
+speclibgen.easypqp.extras.rt_lowess_fraction=0
+speclibgen.easypqp.fragment.a=false
+speclibgen.easypqp.fragment.b=true
+speclibgen.easypqp.fragment.c=false
+speclibgen.easypqp.fragment.x=false
+speclibgen.easypqp.fragment.y=true
+speclibgen.easypqp.fragment.z=false
+speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
+speclibgen.easypqp.neutral_loss=false
+speclibgen.easypqp.rt-cal=ciRT
+speclibgen.easypqp.select-file.text=
+speclibgen.easypqp.select-im-file.text=
+speclibgen.keep-intermediate-files=false
+speclibgen.run-speclibgen=false
+tab-run.delete_calibrated_mzml=false
+tab-run.delete_temp_files=false
+tab-run.sub_mzml_prob_threshold=0.5
+tab-run.write_sub_mzml=false
+tmtintegrator.add_Ref=-1
+tmtintegrator.aggregation_method=0
+tmtintegrator.allow_overlabel=true
+tmtintegrator.allow_unlabeled=true
+tmtintegrator.best_psm=true
+tmtintegrator.channel_num=TMT-6
+tmtintegrator.dont-run-fq-lq=false
+tmtintegrator.glyco_qval=-1
+tmtintegrator.groupby=0
+tmtintegrator.log2transformed=true
+tmtintegrator.max_pep_prob_thres=0
+tmtintegrator.min_ntt=0
+tmtintegrator.min_pep_prob=0.9
+tmtintegrator.min_percent=0.05
+tmtintegrator.min_purity=0.5
+tmtintegrator.min_site_prob=-1
+tmtintegrator.mod_tag=none
+tmtintegrator.ms1_int=true
+tmtintegrator.outlier_removal=true
+tmtintegrator.print_RefInt=false
+tmtintegrator.prot_exclude=none
+tmtintegrator.prot_norm=0
+tmtintegrator.psm_norm=false
+tmtintegrator.quant_level=2
+tmtintegrator.ref_tag=Bridge
+tmtintegrator.run-tmtintegrator=false
+tmtintegrator.tolerance=20
+tmtintegrator.top3_pep=true
+tmtintegrator.unique_gene=0
+tmtintegrator.unique_pep=false
+tmtintegrator.use_glycan_composition=false
+workflow.input.data-type.im-ms=false
+workflow.input.data-type.regular-ms=true
+workflow.saved-with-ver=20.0-build5