Update FragPipe Tool to Version 23.0 (#801)

* Updates for FragPipe version 23.0.

* Updates for automated tests.

* Increase profile version to 24.2 and fix version_command.

* Small changes to standardize XML that don't affect behavior. Remove unnecessary str conversion. Indent koina-url parameter. Compare unset groupby parameter to 'None' as is done for other select parameters.

Author: reid-wagner

tools/fragpipe/fragpipe

@@ -22,6 +22,10 @@ while [[ $# -gt 0 ]]; do
             shift
             ionquant_key=$1
             ;;
+        --diatracer_key)
+            shift
+            diatracer_key=$1
+            ;;
         --workflow)
             fragpipe_args+=("$1")
             shift
@@ -35,16 +39,7 @@ while [[ $# -gt 0 ]]; do
     shift
 done
 
-if [[ ! -z "$workflow_file" ]]; then
-    # Because the DIA-NN license is incompatible with bioconda, we remove the feature.
-    grep 'diann.run-dia-nn=true' "$workflow_file" >/dev/null
-    if [[ $? -eq 0 ]]; then
-        echo "Error: DIA-NN is disabled in the FragPipe bioconda package."
-        exit 1
-    fi
-fi
-
-if [[ -z $msfragger_key || -z $ionquant_key ]]; then
+if [[ -z $msfragger_key || -z $ionquant_key || -z $diatracer_key ]]; then
     echo "$license_agreement_text"
     exit 1
 else
@@ -60,6 +55,12 @@ else
         echo "$license_agreement_text"
         exit 1
     fi
+    diatracer --key $diatracer_key --help | grep 'License key verified' >/dev/null 2>&1
+    if [[ $? -ne 0 ]]; then
+        echo "Error: Invalid diaTracer license key"
+        echo "$license_agreement_text"
+        exit 1
+    fi
 fi
 
 sh fragpipe_local/bin/fragpipe "${fragpipe_args[@]}"

tools/fragpipe/fragpipe.xml

@@ -1,16 +1,34 @@
+# Workflow: Basic-Search
+
+
+crystalc.run-crystalc=false
+database.db-path=final_db.fas
 database.decoy-tag=rev_
-diann.fragpipe.cmd-opts=
+diann.channel-normalization-strategy=0
+diann.cmd-opts=
+diann.generate-msstats=true
 diann.heavy=
 diann.library=
 diann.light=
 diann.medium=
+diann.min-site-prob=0.75
+diann.mod-tag=
 diann.q-value=0.01
 diann.quantification-strategy=3
+diann.quantification-strategy-2=2
 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
+diann.use-predicted-spectra=false
+diatracer.corr-threshold=0.3
+diatracer.delta-apex-im=0.01
+diatracer.delta-apex-rt=3
+diatracer.mass-defect-filter=true
+diatracer.mass-defect-offset=0.1
+diatracer.rf-max=500
+diatracer.run-diatracer=false
+diatracer.write-intermediate-files=false
 diaumpire.AdjustFragIntensity=true
 diaumpire.BoostComplementaryIon=false
 diaumpire.CorrThreshold=0
@@ -32,10 +50,19 @@ diaumpire.SE.MassDefectOffset=0.1
 diaumpire.SE.NoMissedScan=1
 diaumpire.SE.SN=1.1
 diaumpire.run-diaumpire=false
+fpop.coadaptr.fpop.fpop_masses=
+fpop.coadaptr.fpop.run-fpop-coadaptr=false
+fpop.fragpipe.fpop.fpop-tmt=false
+fpop.fragpipe.fpop.label_control=
+fpop.fragpipe.fpop.label_fpop=
+fpop.fragpipe.fpop.region_size=1
+fpop.fragpipe.fpop.run-fpop=false
+fpop.fragpipe.fpop.subtract-control=false
 freequant.mz-tol=10
 freequant.rt-tol=0.4
 freequant.run-freequant=false
 ionquant.excludemods=
+ionquant.formula=
 ionquant.heavy=
 ionquant.imtol=0.05
 ionquant.ionfdr=0.01
@@ -49,7 +76,7 @@ ionquant.mbrrttol=1
 ionquant.mbrtoprun=10
 ionquant.medium=
 ionquant.minfreq=0
-ionquant.minions=2
+ionquant.minions=1
 ionquant.minisotopes=2
 ionquant.minscans=3
 ionquant.mztol=10
@@ -64,15 +91,24 @@ ionquant.uniqueness=0
 ionquant.use-labeling=false
 ionquant.use-lfq=true
 ionquant.writeindex=0
+msbooster.find-best-im-model=false
+msbooster.find-best-rt-model=false
+msbooster.find-best-spectra-model=false
+msbooster.fragmentation-type=0
+msbooster.im-model=DIA-NN
+msbooster.koina-url=
+msbooster.predict-im=true
 msbooster.predict-rt=true
 msbooster.predict-spectra=true
+msbooster.rt-model=DIA-NN
 msbooster.run-msbooster=false
-msbooster.use-correlated-features=false
+msbooster.spectra-model=DIA-NN
+msbooster.spectral-library-path=
 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.analyzer_types=all
 msfragger.calibrate_mass=2
 msfragger.check_spectral_files=true
 msfragger.clip_nTerm_M=true
@@ -94,6 +130,7 @@ msfragger.labile_search_mode=off
 msfragger.localize_delta_mass=false
 msfragger.mass_diff_to_variable_mod=0
 msfragger.mass_offsets=0
+msfragger.mass_offsets_detailed=
 msfragger.max_fragment_charge=2
 msfragger.max_variable_mods_combinations=5000
 msfragger.max_variable_mods_per_peptide=3
@@ -104,8 +141,8 @@ 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.digest-mass-hi=5000.0
+msfragger.misc.fragger.digest-mass-lo=500.0
 msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
 msfragger.misc.fragger.enzyme-dropdown-2=null
 msfragger.misc.fragger.precursor-charge-hi=4
@@ -117,8 +154,8 @@ 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_dda_plus=5
 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
@@ -142,16 +179,17 @@ 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.table.var-mods=15.99491461956,M,true,3; 42.0105646837,[^,true,1
 msfragger.track_zero_topN=0
 msfragger.use_all_mods_in_first_search=false
+msfragger.use_detailed_offsets=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.allowed_sites=
 opair.filterOxonium=true
 opair.glyco_db=
 opair.max_glycans=4
@@ -174,14 +212,14 @@ 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.cmdline=NOSTACK KEEPOLD STATIC FRAGPPMTOL\=10 EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
+ptmprophet.override-defaults=false
 ptmprophet.run-ptmprophet=false
 ptmshepherd.adv_params=false
 ptmshepherd.annotation-common=false
@@ -193,22 +231,18 @@ 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
@@ -218,9 +252,9 @@ ptmshepherd.iontype_c=true
 ptmshepherd.iontype_x=false
 ptmshepherd.iontype_y=true
 ptmshepherd.iontype_z=true
+ptmshepherd.iterloc_maxEpoch=100
+ptmshepherd.iterloc_mode=false
 ptmshepherd.localization_allowed_res=
-ptmshepherd.localization_background=4
-ptmshepherd.max_adducts=0
 ptmshepherd.n_glyco=true
 ptmshepherd.normalization-psms=true
 ptmshepherd.normalization-scans=false
@@ -232,28 +266,41 @@ 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.print_full_glyco_params=false
+ptmshepherd.prob_mass=0.5
 ptmshepherd.remainder_masses=
 ptmshepherd.remove_glycan_delta_mass=true
 ptmshepherd.run-shepherd=false
+ptmshepherd.run_diagextract_mode=false
+ptmshepherd.run_diagmine_mode=false
+ptmshepherd.run_glyco_mode=false
+ptmshepherd.spectra_condPeaks=150
+ptmshepherd.spectra_condRatio=0.0001
+ptmshepherd.spectra_maxPrecursorCharge=4
 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.cmd-opts=
 saintexpress.max-replicates=10
 saintexpress.run-saint-express=false
 saintexpress.virtual-controls=100
+skyline.run-skyline=false
+skyline.skyline=false
+skyline.skyline-custom=false
+skyline.skyline-custom-path=
+skyline.skyline-daily=true
+skyline.skyline-fragment-tolerance=10
+skyline.skyline-mods-mode=Default
+skyline.skyline-precursor-tolerance=10
+skyline.use-ssl=false
+speclibgen.convert-pepxml=true
+speclibgen.convert-psm=false
 speclibgen.easypqp.extras.max_delta_ppm=15
 speclibgen.easypqp.extras.max_delta_unimod=0.02
+speclibgen.easypqp.extras.max_glycan_qval=1
 speclibgen.easypqp.extras.rt_lowess_fraction=0
 speclibgen.easypqp.fragment.a=false
 speclibgen.easypqp.fragment.b=true
@@ -262,6 +309,7 @@ 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.labile_mode=Regular (not glyco)
 speclibgen.easypqp.neutral_loss=false
 speclibgen.easypqp.rt-cal=ciRT
 speclibgen.easypqp.select-file.text=
@@ -270,6 +318,7 @@ speclibgen.keep-intermediate-files=false
 speclibgen.run-speclibgen=false
 tab-run.delete_calibrated_mzml=false
 tab-run.delete_temp_files=false
+tab-run.export_matched_fragments=false
 tab-run.sub_mzml_prob_threshold=0.5
 tab-run.write_sub_mzml=false
 tmtintegrator.add_Ref=-1
@@ -278,24 +327,28 @@ tmtintegrator.allow_overlabel=true
 tmtintegrator.allow_unlabeled=true
 tmtintegrator.best_psm=true
 tmtintegrator.channel_num=TMT-6
-tmtintegrator.dont-run-fq-lq=false
+tmtintegrator.extraction_tool=IonQuant
 tmtintegrator.glyco_qval=-1
-tmtintegrator.groupby=0
+tmtintegrator.groupby=-1
 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_resolution=0
 tmtintegrator.min_site_prob=-1
+tmtintegrator.min_snr=0
 tmtintegrator.mod_tag=none
 tmtintegrator.ms1_int=true
 tmtintegrator.outlier_removal=true
+tmtintegrator.philosopher-msstats=false
 tmtintegrator.print_RefInt=false
 tmtintegrator.prot_exclude=none
 tmtintegrator.prot_norm=0
 tmtintegrator.psm_norm=false
 tmtintegrator.quant_level=2
+tmtintegrator.ref_d_tag=Pool
 tmtintegrator.ref_tag=Bridge
 tmtintegrator.run-tmtintegrator=false
 tmtintegrator.tolerance=20
@@ -305,4 +358,6 @@ 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
+workflow.misc.save-sdrf=true
+workflow.misc.sdrf-type=Default
+workflow.saved-with-ver=23.0-build14