# HG changeset patch
# User galaxyp
# Date 1743375660 0
# Node ID 2e667f0ec33ca7e25b776543922f6fa0f50198a7
# Parent 048390db193255ebe5231ac3602da509ced050bb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
diff -r 048390db1932 -r 2e667f0ec33c fragpipe.xml
--- a/fragpipe.xml Sat Feb 01 18:12:08 2025 +0000
+++ b/fragpipe.xml Sun Mar 30 23:01:00 2025 +0000
@@ -153,10 +153,10 @@
<param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/>
<param name="database_name" value="default/test.fasta" ftype="fasta"/>
<param name="manifest" value="default/test.manifest" ftype="tabular"/>
- <param name="workflow_name" value="Default"/>
- <param name="label_free_quantification_run" value="ionquant"/>
+ <param name="wf|workflow_name" value="Default"/>
<param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/>
<param name="license_agreements" value="true"/>
+ <param name="wf|validation|validation_tab|psm_validation|run_psm_validation" value="percolator"/>
<output name="concat_psm_tsv" ftype="tabular">
<assert_contents>
<has_text text="Experiment	Spectrum	Spectrum File	Peptide	Modified Peptide	Extended Peptide	Prev AA	Next AA	Peptide Length	Charge	Retention	Observed Mass	Calibrated Observed Mass	Observed M/Z	Calibrated Observed M/Z	Calculated Peptide Mass	Calculated M/Z	Delta Mass	Expectation	Hyperscore	Nextscore	PeptideProphet Probability	Number of Enzymatic Termini	Number of Missed Cleavages	Protein Start	Protein End	Intensity	Assigned Modifications	Observed Modifications	Purity	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/>
@@ -203,11 +203,30 @@
<param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/>
<param name="database_name" value="default/test.fasta" ftype="fasta"/>
<param name="manifest" value="default/test.manifest" ftype="tabular"/>
- <param name="workflow_name" value="Default"/>
- <param name="label_free_quantification_run" value="ionquant"/>
+ <param name="wf|workflow_name" value="Nonspecific-HLA"/>
<param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/>
<param name="license_agreements" value="true"/>
- <param name="run_psm_validation" value="msbooster_percolator"/>
+ <output name="output_workflow" ftype="txt" file="nonspecific-hla/outputs/workflow.txt" compare="contains">
+ <assert_contents>
+ <has_text text="crystalc.run-crystalc=false"/>
+ </assert_contents>
+ </output>
+ <output name="concat_protein_tsv" ftype="tabular">
+ <assert_contents>
+ <has_text text="sample1"/>
+ <!-- Check for match from decoy_and_contam option -->
+ <has_text text="sp|P01375|TNFA_HUMAN"/>
+ </assert_contents>
+ </output>
+ </test>
+ <test expect_num_outputs="11">
+ <param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/>
+ <param name="database_name" value="default/test.fasta" ftype="fasta"/>
+ <param name="manifest" value="default/test.manifest" ftype="tabular"/>
+ <param name="wf|workflow_name" value="Default"/>
+ <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/>
+ <param name="license_agreements" value="true"/>
+ <param name="wf|validation|validation_tab|psm_validation|run_psm_validation" value="msbooster_percolator"/>
<output name="concat_psm_tsv" ftype="tabular">
<assert_contents>
<has_text text="Experiment	Spectrum	Spectrum File	Peptide	Modified Peptide	Extended Peptide	Prev AA	Next AA	Peptide Length	Charge	Retention	Observed Mass	Calibrated Observed Mass	Observed M/Z	Calibrated Observed M/Z	Calculated Peptide Mass	Calculated M/Z	Delta Mass	SpectralSim	RTScore	Expectation	Hyperscore	Nextscore	PeptideProphet Probability	Number of Enzymatic Termini	Number of Missed Cleavages	Protein Start	Protein End	Intensity	Assigned Modifications	Observed Modifications	Purity	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/>
@@ -254,13 +273,13 @@
<param name="inputs" value="tmt11/test1.mzML,tmt11/test2.mzML" ftype="mzml"/>
<param name="database_name" value="tmt11/test.fasta" ftype="fasta"/>
<param name="manifest" value="tmt11/test.manifest" ftype="tabular"/>
- <param name="annotation" value="tmt11/test.annotation" ftype="tabular"/>
- <param name="workflow_name" value="TMT11"/>
+ <param name="wf|annotation" value="tmt11/test.annotation" ftype="tabular"/>
+ <param name="wf|workflow_name" value="TMT11"/>
<param name="output_options" value="workflow,log,concatenated_outputs"/>
<param name="license_agreements" value="true"/>
<output name="concat_psm_tsv" ftype="tabular">
<assert_contents>
- <has_text text="Experiment	Spectrum	Spectrum File	Peptide	Modified Peptide	Extended Peptide	Prev AA	Next AA	Peptide Length	Charge	Retention	Observed Mass	Calibrated Observed Mass	Observed M/Z	Calibrated Observed M/Z	Calculated Peptide Mass	Calculated M/Z	Delta Mass	Expectation	Hyperscore	Nextscore	PeptideProphet Probability	Number of Enzymatic Termini	Number of Missed Cleavages	Protein Start	Protein End	Intensity	Assigned Modifications	Observed Modifications	Purity	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/>
+ <has_text text="Experiment	Spectrum	Spectrum File	Peptide	Modified Peptide	Extended Peptide	Prev AA	Next AA	Peptide Length	Charge	Retention	Observed Mass	Calibrated Observed Mass	Observed M/Z	Calibrated Observed M/Z	Calculated Peptide Mass	Calculated M/Z	Delta Mass	SpectralSim	RTScore	Expectation	Hyperscore	Nextscore	PeptideProphet Probability	Number of Enzymatic Termini	Number of Missed Cleavages	Protein Start	Protein End	Intensity	Assigned Modifications	Observed Modifications	Purity	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/>
<has_text text="sample1"/>
</assert_contents>
</output>
diff -r 048390db1932 -r 2e667f0ec33c macros.xml
--- a/macros.xml Sat Feb 01 18:12:08 2025 +0000
+++ b/macros.xml Sun Mar 30 23:01:00 2025 +0000
@@ -1,7 +1,7 @@
<macros>
<import>msfragger_macros.xml</import>
<token name="@TOOL_VERSION@">20.0</token>
- <token name="@VERSION_SUFFIX@">5</token>
+ <token name="@VERSION_SUFFIX@">6</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement>
@@ -84,7 +84,7 @@
#if str($database_options) != 'none'
philosopher workspace --init &&
philosopher database --custom genericized_db.fas --prefix rev_
- #if str($database_options) != 'decoy_and_contam'
+ #if str($database_options) == 'decoy_and_contam'
--contam
#end if
--contamprefix &&
@@ -166,8 +166,8 @@
</section>
<expand macro="validation"
pep="false"
- perc="true"
- boost="false"
+ perc="false"
+ boost="true"
no="false"
masswidth="5"
clevel="0"
@@ -212,8 +212,8 @@
</section>
<expand macro="validation"
pep="false"
- perc="true"
- boost="false"
+ perc="false"
+ boost="true"
no="true"
masswidth="5"
clevel="0"
@@ -232,11 +232,10 @@
<section name="msfragger" expanded="false" title="MSFragger Options">
<expand macro="msfragger_LFQ_MBR"/>
</section>
- <!-- MSBooster should be enabled once included in FragPipe Galaxy tool -->
<expand macro="validation"
pep="false"
- perc="true"
- boost="false"
+ perc="false"
+ boost="true"
no="true"
masswidth="5"
clevel="0"
@@ -270,8 +269,8 @@
</section>
<expand macro="validation"
pep="false"
- perc="true"
- boost="false"
+ perc="false"
+ boost="true"
no="false"
masswidth="5"
clevel="0"
@@ -524,11 +523,11 @@
#elif $prfx.run_psm_validation == 'percolator'
#set $wfdict['run-psm-validation'] = 'true'
#set $wfdict['msbooster.run-msbooster'] = 'false'
- #set $wfdict['peptide-prophet.run-peptide-prophet=false'] = 'false'
+ #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
@PERCOLATOR@
#elif $prfx.run_psm_validation == 'msbooster_percolator'
#set $wfdict['run-psm-validation'] = 'true'
- #set $wfdict['peptide-prophet.run-peptide-prophet=false'] = 'false'
+ #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
@MSBOOSTER@
@PERCOLATOR@
#end if
diff -r 048390db1932 -r 2e667f0ec33c msfragger_macros.xml
--- a/msfragger_macros.xml Sat Feb 01 18:12:08 2025 +0000
+++ b/msfragger_macros.xml Sun Mar 30 23:01:00 2025 +0000
@@ -61,7 +61,7 @@
</xml>
<xml name="msfragger_nonspecific_HLA">
<expand macro="search_tolerances" precursor_mass_lower="-20" precursor_mass_upper="20"/>
- <expand macro="digestion" stricttrypsin="false" nonspecific="true" digest_max_length="25" termini_0="true" termini_2="false"/>
+ <expand macro="digestion" stricttrypsin="false" nonspecific="true" digest_max_length="25" termini_0="true" termini_2="false" digest_mass_range_min="200.0"/>
<expand macro="variable_modification"/>
<expand macro="static_modification"/>
<expand macro="glyco_labile"/>
diff -r 048390db1932 -r 2e667f0ec33c test-data/nonspecific-hla/outputs/workflow.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nonspecific-hla/outputs/workflow.txt Sun Mar 30 23:01:00 2025 +0000
@@ -0,0 +1,309 @@
+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=false
+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=true
+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=25
+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=1
+msfragger.ion_series_definitions=
+msfragger.isotope_error=0/1
+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=5
+msfragger.min_sequence_matches=2
+msfragger.minimum_peaks=15
+msfragger.minimum_ratio=0.00
+msfragger.misc.fragger.clear-mz-hi=0.0
+msfragger.misc.fragger.clear-mz-lo=0.0
+msfragger.misc.fragger.digest-mass-hi=5000.0
+msfragger.misc.fragger.digest-mass-lo=200.0
+msfragger.misc.fragger.enzyme-dropdown-1=nonspecific
+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=0
+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=15
+msfragger.precursor_true_units=1
+msfragger.remainder_fragment_masses=-18.01056 79.96633
+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=-
+msfragger.search_enzyme_cut_2=-
+msfragger.search_enzyme_name_1=nonspecific
+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),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
+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
+msfragger.track_zero_topN=0
+msfragger.use_all_mods_in_first_search=false
+msfragger.use_topN_peaks=300
+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 --prot 1
+phi-report.pep-level-summary=true
+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=
+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=false
+ptmshepherd.iontype_x=false
+ptmshepherd.iontype_y=true
+ptmshepherd.iontype_z=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
+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=noiRT
+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.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>
+workflow.input.data-type.im-ms=false
+workflow.input.data-type.regular-ms=true
+workflow.saved-with-ver=20.0-build5
diff -r 048390db1932 -r 2e667f0ec33c test-data/tmt11/outputs/workflow.txt
--- a/test-data/tmt11/outputs/workflow.txt Sat Feb 01 18:12:08 2025 +0000
+++ b/test-data/tmt11/outputs/workflow.txt Sun Mar 30 23:01:00 2025 +0000
@@ -66,7 +66,7 @@
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
-msbooster.run-msbooster=false
+msbooster.run-msbooster=true
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all