Tool name	Added/removed	Parameter name	Type	Default value	Restrictions	Supported formats
AssayGeneratorMetabo	+	preprocessing:precursor_mz_tolerance	double	5.0e-03		
AssayGeneratorMetabo	-	preprocessing:precursor_mz_tolerance	double	0.005		
CometAdapter	+	binary_modifications	int			
CometAdapter	+	enzyme	string	Trypsin	Lys-N,Lys-C,glutamyl endopeptidase,unspecific cleavage,Arg-C,Asp-N,Trypsin,PepsinA,Chymotrypsin,CNBr,Trypsin/P	
CometAdapter	+	fragment_error_units	string	Da	Da	
CometAdapter	+	fragment_mass_tolerance	double	0.01	1.0e-04:	
CometAdapter	+	isotope_error	string	off	off,0/1,0/1/2,0/1/2/3,-8/-4/0/4/8	
CometAdapter	+	max_peptide_length	int	63	5:63	
CometAdapter	+	min_peptide_length	int	5	5:63	
CometAdapter	+	missed_cleavages	int	1	0:5	
CometAdapter	+	num_hits	int	1		
CometAdapter	+	second_enzyme	string		Lys-N,Lys-C,glutamyl endopeptidase,unspecific cleavage,Arg-C,Asp-N,Trypsin,PepsinA,Chymotrypsin,CNBr,Trypsin/P	
CometAdapter	-	allowed_missed_cleavages	int	0	0:5	
CometAdapter	-	comet_version	string	2016.01 rev. 2		
CometAdapter	-	enzyme	string	Trypsin	Trypsin,Arg-C,Asp-N,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,unspecific cleavage	
CometAdapter	-	fragment_bin_tolerance	double	0.02	0.01:	
CometAdapter	-	isotope_error	string	off	off,0/1,0/1/2,-1/0/1/2/3,-8/-4/0/4/8	
CometAdapter	-	num_hits	int	5		
ConsensusID	+	filter:keep_old_scores	bool	false		
ConsensusID	+	in	input-file			*.idXML,*.featureXML,*.consensusXML
ConsensusID	+	per_spectrum	bool	false		
ConsensusID	-	in	input-file			*.idXML,*.featureXML,*.consensusXML
ConsensusMapNormalizer	+	ratio_threshold	double	0.67	1.0e-03:1.0	
ConsensusMapNormalizer	-	ratio_threshold	double	0.67	0.001:1.0	
CruxAdapter	+	decoy_format	string	shuffle	none,shuffle,peptide-reverse,protein-reverse	
CruxAdapter	+	enzyme	string	trypsin	custom-enzyme,lys-n,asp-n,lys-c,arg-c,trypsin/p,elastase,iodosobenzoate,trypsin,staph-protease,proline-endopeptidase,glu-c,pepsin-a,chymotrypsin,clostripain,elastase-trypsin-chymotrypsin,no-enzyme,cyanogen-bromide	
CruxAdapter	+	keep_terminal_aminos	string	NC	N,C,NC,none	
CruxAdapter	-	decoy-format	string	shuffle	none,shuffle,peptide-reverse,protein-reverse	
CruxAdapter	-	enzyme	string	trypsin	custom-enzyme,arg-c,iodosobenzoate,staph-protease,proline-endopeptidase,glu-c,pepsin-a,cyanogen-bromide,clostripain,elastase,lys-c,chymotrypsin,trypsin,trypsin/p,asp-n,elastase-trypsin-chymotrypsin,no-enzyme,lys-n	
CruxAdapter	-	keep-terminal-aminos	string	NC	N,C,NC,none	
DecoyDatabase	+	enzyme	string	Trypsin	proline-endopeptidase/HKR,Clostripain/P,Glu-C+P,PepsinA + P,cyanogen-bromide,no cleavage,unspecific cleavage,elastase-trypsin-chymotrypsin,staphylococcal protease/D,Arg-C/P,Trypsin,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,Formic_acid,V8-E,Lys-C/P,PepsinA,Lys-C,CNBr,TrypChymo,Lys-N,V8-DE,Trypsin/P	
DecoyDatabase	-	enzyme	string	Trypsin	Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,Arg-C/P,Trypsin,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
Digestor	+	enzyme	string	Trypsin	V8-DE,Arg-C/P,Trypsin,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-E,iodosobenzoate,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
Digestor	-	enzyme	string	Trypsin	Arg-C,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,Arg-C/P,Trypsin,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
DigestorMotif	+	enzyme	string	Trypsin	proline endopeptidase,leukocyte elastase,V8-E,V8-DE,TrypChymo,PepsinA,Trypsin/P,Asp-N,Asp-N/B,Asp-N_ambic,CNBr,Chymotrypsin,Chymotrypsin/P,Alpha-lytic protease,Formic_acid,Lys-C,Lys-N,Lys-C/P,iodosobenzoate,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Trypsin,Arg-C/P,glutamyl endopeptidase	
DigestorMotif	-	enzyme	string	Trypsin	glutamyl endopeptidase,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Lys-N,PepsinA + P,cyanogen-bromide,Lys-C/P,Arg-C/P,PepsinA,Arg-C,Chymotrypsin/P,proline endopeptidase,Asp-N,Clostripain/P,elastase-trypsin-chymotrypsin,Trypsin,Lys-C,no cleavage,leukocyte elastase,unspecific cleavage,Asp-N/B,CNBr,2-iodobenzoate,iodosobenzoate,TrypChymo,Chymotrypsin,Alpha-lytic protease,Formic_acid,Asp-N_ambic,Trypsin/P,V8-DE,V8-E	
Epifany	+	algorithm:keep_best_PSM_only	string	true	true,false	
Epifany	+	algorithm:loopy_belief_propagation:dampening_lambda	double	1.0e-03	0.0:0.49999	
Epifany	+	algorithm:loopy_belief_propagation:scheduling_type	string	priority	priority,fifo,subtree	
Epifany	+	algorithm:param_optimize:regularized_fdr	string	true	true,false	
Epifany	+	algorithm:psm_probability_cutoff	double	1.0e-03	0.0:1.0	
Epifany	+	exp_design	input-file			*.tsv
Epifany	+	in	input-file			*.idXML,*.consensusXML
Epifany	+	out	output-file			*.idXML,*.consensusXML
Epifany	+	out_type	string		idXML,consensusXML	
Epifany	-	algorithm:loopy_belief_propagation:dampening_lambda	double	0.001	0.0:0.49999	
Epifany	-	algorithm:loopy_belief_propagation:scheduling_type	string	priority	priority,fifo,random_spanning_tree	
Epifany	-	algorithm:psm_probability_cutoff	double	0.001	0.0:1.0	
Epifany	-	in	input-file			*.idXML
Epifany	-	out	output-file			*.idXML
FeatureFinderIdentification	+	model:each_trace	bool	false		
FeatureFinderIdentification	+	svm:epsilon	double	1.0e-03	0.0:	
FeatureFinderIdentification	-	svm:epsilon	double	0.001	0.0:	
FeatureFinderMetabo	+	algorithm:epd:min_fwhm	double	1.0		
FeatureFinderMetabo	-	algorithm:epd:min_fwhm	double	3.0		
FeatureFinderMetaboIdent	+	model:each_trace	bool	false		
FileFilter	+	id:mz	double	1.0e-03	0.0:	
FileFilter	-	id:mz	double	0.001	0.0:	
FileInfo	+	in	input-file			*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML,*.fasta,*.pqp
FileInfo	+	in_type	string		mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid,trafoXML,fasta,pqp	
FileInfo	-	in	input-file			*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML,*.fasta
FileInfo	-	in_type	string		mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid,trafoXML	
IDFileConverter	+	concatenate_peptides	bool	false		
IDFileConverter	+	number_of_hits	int	1		
IDFilter	+	in	input-file			*.idXML,*.consensusXML
IDFilter	+	in_silico_digestion:enzyme	string	Trypsin	Formic_acid,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,iodosobenzoate,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Arg-C,Trypsin,no cleavage,unspecific cleavage,CNBr	
IDFilter	+	in_silico_digestion:specificity	string	full	none,semi,full	
IDFilter	+	missed_cleavages:enzyme	string	Trypsin	Formic_acid,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,iodosobenzoate,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Arg-C,Trypsin,no cleavage,unspecific cleavage,CNBr	
IDFilter	+	out	output-file			*.idXML,*.consensusXML
IDFilter	+	score:protgroup	double	0.0		
IDFilter	-	in	input-file			*.idXML
IDFilter	-	in_silico_digestion:enzyme	string	Trypsin	Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Asp-N_ambic,Trypsin,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C/P,Arg-C,Asp-N,Asp-N/B	
IDFilter	-	in_silico_digestion:specificity	string	full	full,semi,none	
IDFilter	-	missed_cleavages:enzyme	string	Trypsin	Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Asp-N_ambic,Trypsin,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C/P,Arg-C,Asp-N,Asp-N/B	
IDFilter	-	out	output-file			*.idXML
InspectAdapter	+	in	input-file			*.mzXML,*.mzData,*.txt
InspectAdapter	+	inspect_input	input-file			*.txt
InspectAdapter	+	inspect_output	output-file			*.txt
InspectAdapter	+	out	output-file			*.idXML,*.txt
InspectAdapter	-	in	input-file			*.mzXML,*.mzData
InspectAdapter	-	inspect_input	input-file			
InspectAdapter	-	inspect_output	output-file			
InspectAdapter	-	out	output-file			*.idXML
IsobaricAnalyzer	+	extraction:reporter_mass_shift	double	2.0e-03	1.0e-04:0.5	
IsobaricAnalyzer	-	extraction:reporter_mass_shift	double	0.002	1.0e-04:0.5	
MRMMapper	+	tr	input-file			*.traML
MRMMapper	-	tr	input-file			*.TraML
MRMTransitionGroupPicker	+	algorithm:minimal_quality	double	-1.0e04		
MRMTransitionGroupPicker	-	algorithm:minimal_quality	double	-10000.0		
MSFraggerAdapter	+	digest:search_enzyme_name	string	Trypsin	Arg-C,Arg-C/P,Asp-N/B,Trypsin,Chymotrypsin,Asp-N_ambic,Asp-N,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
MSFraggerAdapter	+	executable	input-file	MSFragger.jar		
MSFraggerAdapter	-	digest:search_enzyme_name	string	Trypsin	Arg-C/P,Asp-N/B,Asp-N_ambic,Chymotrypsin,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,PepsinA + P,cyanogen-bromide,Clostripain/P,PepsinA,TrypChymo,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,proline endopeptidase,leukocyte elastase,Asp-N,Trypsin/P,V8-DE,V8-E,Lys-N,Lys-C/P,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Arg-C,Trypsin,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
MSFraggerAdapter	-	executable	input-file			
MSGFPlusAdapter	+	conf	input-file			
MSGFPlusAdapter	+	max_missed_cleavages	int	-1	-1:	
MSGFPlusAdapter	+	tasks	int	0		
MSSimulator	+	algorithm:MSSim:Digestion:enzyme	string	Trypsin	TrypChymo,V8-DE,Trypsin/P,V8-E,Arg-C/P,Trypsin,Arg-C,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,proline-endopeptidase/HKR,staphylococcal protease/D,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,no cleavage,unspecific cleavage,elastase-trypsin-chymotrypsin	
MSSimulator	-	algorithm:MSSim:Digestion:enzyme	string	Trypsin	Lys-N,Lys-C,Arg-C/P,Trypsin,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Lys-C/P,Formic_acid,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,no cleavage,elastase-trypsin-chymotrypsin,unspecific cleavage	
MapAlignerPoseClustering	+	algorithm:superimposer:scaling_bucket_size	double	5.0e-03	0.0:	
MapAlignerPoseClustering	-	algorithm:superimposer:scaling_bucket_size	double	0.005	0.0:	
MapAlignerTreeGuided	+	copy_data	string	true	true,false	
MascotAdapter	+	in	input-file			*.mzData,*.mascotXML
MascotAdapter	+	out	output-file			*.idXML,*.mgf
MascotAdapter	+	out_type	string		idXML,mgf	
MascotAdapter	-	in	input-file			
MascotAdapter	-	mascot_in	bool	false		
MascotAdapter	-	mascot_out	bool	false		
MascotAdapter	-	out	output-file			
MassCalculator	+	in	input-file			*.tsv
MassCalculator	+	out	output-file			*.csv
MassCalculator	-	in	input-file			*.txt
MassCalculator	-	out	output-file			*.txt
MassTraceExtractor	+	algorithm:epd:min_fwhm	double	1.0		
MassTraceExtractor	-	algorithm:epd:min_fwhm	double	3.0		
MyriMatchAdapter	+	MaxPeptideMass	double	1.0e04		
MyriMatchAdapter	-	MaxPeptideMass	double	10000.0		
NovorAdapter	+	in	input-file			*.mzML
NovorAdapter	-	in	input-file			*.mzml
NucleicAcidSearchEngine	+	oligo:enzyme	string	no cleavage	RNase_T1,RNase_U2,cusativin,RNase_A,RNase_MC1,RNase_H,no cleavage,unspecific cleavage	
NucleicAcidSearchEngine	-	oligo:enzyme	string	no cleavage	unspecific cleavage,RNase_T1,cusativin,RNase_U2,RNase_A,RNase_MC1,RNase_H,no cleavage	
OMSSAAdapter	+	enzyme	string	Trypsin	Formic_acid,Lys-C/P,PepsinA,Lys-C,Arg-C,Trypsin,Asp-N,CNBr,Chymotrypsin,Asp-N_ambic,glutamyl endopeptidase,no cleavage,unspecific cleavage,TrypChymo,Trypsin/P	
OMSSAAdapter	-	enzyme	string	Trypsin	Trypsin,Arg-C,Asp-N,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,glutamyl endopeptidase,no cleavage,unspecific cleavage	
OpenPepXL	+	peptide:enzyme	string	Trypsin	cyanogen-bromide,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Clostripain/P,Arg-C,Trypsin,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
OpenPepXL	-	peptide:enzyme	string	Trypsin	Trypsin/P,V8-DE,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,proline-endopeptidase/HKR,staphylococcal protease/D,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Arg-C,Trypsin	
OpenPepXLLF	+	peptide:enzyme	string	Trypsin	Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Arg-C,Trypsin,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
OpenPepXLLF	-	peptide:enzyme	string	Trypsin	Asp-N/B,Arg-C/P,Trypsin,Arg-C,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:minimal_quality	double	-1.0e04		
OpenSwathAnalyzer	+	algorithm:spacing_for_spectra_resampling	double	5.0e-03	0.0:	
OpenSwathAnalyzer	+	tr	input-file			*.traML
OpenSwathAnalyzer	-	algorithm:TransitionGroupPicker:minimal_quality	double	-10000.0		
OpenSwathAnalyzer	-	algorithm:spacing_for_spectra_resampling	double	0.005	0.0:	
OpenSwathAnalyzer	-	tr	input-file			*.TraML
OpenSwathDIAPreScoring	+	output_files	output-file			*.tsv
OpenSwathDIAPreScoring	+	tr	input-file			*.traML
OpenSwathDIAPreScoring	-	out	output-file			*.tsv
OpenSwathDIAPreScoring	-	tr	input-file			*.TraML
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:minimal_quality	double	-1.0e04		
OpenSwathRTNormalizer	+	algorithm:spacing_for_spectra_resampling	double	5.0e-03	0.0:	
OpenSwathRTNormalizer	-	algorithm:TransitionGroupPicker:minimal_quality	double	-10000.0		
OpenSwathRTNormalizer	-	algorithm:spacing_for_spectra_resampling	double	0.005	0.0:	
OpenSwathWorkflow	+	Scoring:spacing_for_spectra_resampling	double	5.0e-03	0.0:	
OpenSwathWorkflow	-	Scoring:spacing_for_spectra_resampling	double	0.005	0.0:	
OpenSwathWorkflow	-	use_ms1_traces	bool	false		
OpenSwathWorkflow	+	enable_ms1	true	true,false	
OpenSwathWorkflow	-	enable_uis_scoring	bool	false		
OpenSwathWorkflow	+	enable_ipf	true	true,false	
OpenSwathWorkflow	-	mz_extraction_window	double	0.05	0.0:	
OpenSwathWorkflow	+	mz_extraction_window	double	50.0	0.0:	
OpenSwathWorkflow	+	mz_extraction_window_unit	string	ppm	Th,ppm	
OpenSwathWorkflow	-	mz_extraction_window_unit	string	Th	Th,ppm	
OpenSwathWorkflow	-	mz_extraction_window_ms1	double	0.05	0.0:	
OpenSwathWorkflow	+	mz_extraction_window_ms1	double	50.0	0.0:	
OpenSwathWorkflow	+	mz_extraction_window_ms1_unit	string	ppm	Th,ppm	
OpenSwathWorkflow	-	mz_extraction_window_ms1_unit	string	Th	Th,ppm	
OpenSwathWorkflow	-	irt_mz_extraction_window	double	0.05	0.0:	
OpenSwathWorkflow	+	irt_mz_extraction_window	double	50.0	0.0:	
OpenSwathWorkflow	+	irt_mz_extraction_window_unit	string	ppm	Th,ppm	
OpenSwathWorkflow	-	irt_mz_extraction_window_unit	string	Th	Th,ppm	
OpenSwathWorkflow	+	batchSize	string	int	1000	0:	
OpenSwathWorkflow	-	batchSize	string	int	250	0:	
OpenSwathWorkflow	+	ms1_isotopes	int	3	0:		
OpenSwathWorkflow	-	ms1_isotopes	int	0	0:	
PSMFeatureExtractor	+	in	input-file			*.idXML,*.mzid
PSMFeatureExtractor	+	out	output-file			*.idXML,*.mzid
PSMFeatureExtractor	+	out_type	string		idXML,mzid	
PSMFeatureExtractor	-	in	input-file			*.mzid,*.idXML
PSMFeatureExtractor	-	out	output-file			*.mzid,*.idXML
PSMFeatureExtractor	-	out_type	string		mzid,idXML	
PTModel	+	out_oligo_params	output-file			*.paramXML
PTModel	+	out_oligo_trainset	output-file			*.txt
PTPredict	+	in_oligo_params	input-file			*.paramXML
PTPredict	+	in_oligo_trainset	input-file			*.txt
PeakPickerWavelet	+	algorithm:wavelet_transform:spacing	double	1.0e-03	0.0:	
PeakPickerWavelet	-	algorithm:wavelet_transform:spacing	double	0.001	0.0:	
PeptideIndexer	+	enzyme:name	string	auto	auto,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Trypsin,V8-DE,V8-E,iodosobenzoate,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C/P,Arg-C,TrypChymo,Trypsin/P,PepsinA,Lys-N,Lys-C/P	
PeptideIndexer	+	enzyme:specificity	string	auto	auto,full,semi,none	
PeptideIndexer	+	unmatched_action	string	error	error,warn,remove	
PeptideIndexer	-	allow_unmatched	bool	false		
PeptideIndexer	-	enzyme:name	string	Trypsin	Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,Arg-C/P,Asp-N,Trypsin,Arg-C,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
PeptideIndexer	-	enzyme:specificity	string	full	full,semi,none	
PercolatorAdapter	+	decoy_pattern	string	random		
PercolatorAdapter	+	default_direction	string			
PercolatorAdapter	+	generic_feature_set	bool	false		
PercolatorAdapter	+	init_weights	input-file			*.tsv
PercolatorAdapter	+	nested_xval_bins	int	1		
PercolatorAdapter	+	out	output-file			*.idXML,*.mzid,*.osw
PercolatorAdapter	+	out_pout_decoy	output-file			*.tab
PercolatorAdapter	+	out_pout_decoy_proteins	output-file			*.tab
PercolatorAdapter	+	out_pout_target	output-file			*.tab
PercolatorAdapter	+	out_pout_target_proteins	output-file			*.tab
PercolatorAdapter	+	peptide_level_fdrs	bool	false		
PercolatorAdapter	+	post_processing_tdc	bool	false		
PercolatorAdapter	+	protein_level_fdrs	bool	false		
PercolatorAdapter	+	quick_validation	bool	false		
PercolatorAdapter	+	static	bool	false		
PercolatorAdapter	+	subset_max_train	int	0		
PercolatorAdapter	+	test_each_iteration	bool	false		
PercolatorAdapter	+	train_best_positive	bool	false		
PercolatorAdapter	+	weights	output-file			*.tsv
PercolatorAdapter	-	decoy-pattern	string	random		
PercolatorAdapter	-	default-direction	string			
PercolatorAdapter	-	generic-feature-set	bool	false		
PercolatorAdapter	-	init-weights	input-file			
PercolatorAdapter	-	out	output-file			*.mzid,*.idXML,*.osw
PercolatorAdapter	-	peptide-level-fdrs	bool	false		
PercolatorAdapter	-	post-processing-tdc	bool	false		
PercolatorAdapter	-	protein-level-fdrs	bool	false		
PercolatorAdapter	-	quick-validation	bool	false		
PercolatorAdapter	-	subset-max-train	int	0		
PercolatorAdapter	-	test-each-iteration	bool	false		
PercolatorAdapter	-	train-best-positive	bool	false		
PercolatorAdapter	-	weights	output-file			
PhosphoScoring	+	out	output-file			*.idXML
PhosphoScoring	-	out	output-file			
ProteinInference	+	Merging:allow_disagreeing_settings	bool	false		
ProteomicsLFQ	+	Linking:distance_MZ:max_difference	double	10.0	0.0:	
ProteomicsLFQ	+	Linking:distance_MZ:unit	string	ppm	Da,ppm	
ProteomicsLFQ	+	Linking:distance_MZ:weight	double	5.0	0.0:	
ProteomicsLFQ	+	Linking:distance_intensity:weight	double	0.1	0.0:	
ProteomicsLFQ	+	Linking:use_identifications	string	true	true,false	
ProteomicsLFQ	+	PeptideQuantification:model:each_trace	bool	false		
ProteomicsLFQ	+	PeptideQuantification:svm:epsilon	double	1.0e-03	0.0:	
ProteomicsLFQ	+	PeptideQuantification:svm:min_prob	double	0.9	0.0:1.0	
ProteomicsLFQ	+	PeptideQuantification:svm:samples	int	10000	0:	
ProteomicsLFQ	+	keep_feature_top_psm_only	string	true	true,false	
ProteomicsLFQ	+	mass_recalibration	bool	false		
ProteomicsLFQ	+	quantification_method	string	feature_intensity	feature_intensity,spectral_counting	
ProteomicsLFQ	+	seedThreshold	double	1.0e04		
ProteomicsLFQ	+	transfer_ids	string	false	false,mean	
ProteomicsLFQ	-	Linking:distance_MZ:max_difference	double	0.3	0.0:	
ProteomicsLFQ	-	Linking:distance_MZ:unit	string	Da	Da,ppm	
ProteomicsLFQ	-	Linking:distance_MZ:weight	double	1.0	0.0:	
ProteomicsLFQ	-	Linking:distance_RT:max_difference	double	100.0	0.0:	
ProteomicsLFQ	-	Linking:distance_intensity:weight	double	0.0	0.0:	
ProteomicsLFQ	-	Linking:use_identifications	bool	false		
ProteomicsLFQ	-	PeptideQuantification:detect:peak_width	double	60.0	0.0:	
ProteomicsLFQ	-	PeptideQuantification:svm:epsilon	double	0.001	0.0:	
ProteomicsLFQ	-	PeptideQuantification:svm:min_prob	double	0.0	0.0:1.0	
ProteomicsLFQ	-	PeptideQuantification:svm:samples	int	0	0:	
ProteomicsLFQ	-	mass_recalibration	string	true	true,false	
ProteomicsLFQ	-	transfer_ids	string	false	false,merged,SVM	
QualityControl	+	MS2_id_rate:assume_all_target	bool	false		
QualityControl	-	MS2_id_rate:force_no_fdr	bool	false		
RNADigestor	+	enzyme	string	RNase_T1	RNase_A,RNase_U2,RNase_MC1,RNase_H,no cleavage,unspecific cleavage,cusativin,RNase_T1	
RNADigestor	-	enzyme	string	RNase_T1	RNase_H,no cleavage,unspecific cleavage,RNase_T1,RNase_A,cusativin,RNase_MC1,RNase_U2	
RNAMassCalculator	+	format	string	list	list,table,mass_only,mz_only,formula_only	
RNAMassCalculator	-	format	string	list	list,table,mass_only,mz_only	
RNPxlSearch	+	peptide:enzyme	string	Trypsin	Asp-N_ambic,CNBr,Formic_acid,V8-DE,Chymotrypsin/P,Asp-N,Asp-N/B,Glu-C+P,Arg-C,Arg-C/P,Trypsin,no cleavage,unspecific cleavage,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Chymotrypsin,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-E,proline endopeptidase,leukocyte elastase,Alpha-lytic protease,2-iodobenzoate,glutamyl endopeptidase	
RNPxlSearch	-	peptide:enzyme	string	Trypsin	Arg-C/P,Trypsin,Arg-C,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,iodosobenzoate,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
RTEvaluation	+	out	output-file			*.tsv
RTEvaluation	-	out	output-file			*.csv
SemanticValidator	+	in	input-file			*.analysisXML,*.mzML,*.traML,*.mzid,*.mzData,*.xml
SemanticValidator	-	in	input-file			*.analysisXML,*.mzML,*.TraML,*.mzid,*.mzData,*.xml
SimpleSearchEngine	+	Search:annotate:PSM	string		fragment_mz_error_median_ppm,precursor_mz_error_ppm	
SimpleSearchEngine	+	Search:decoys	bool	false		
SimpleSearchEngine	+	Search:enzyme	string	Trypsin	V8-DE,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-E,Trypsin/P,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Asp-N,Asp-N/B,Arg-C,Arg-C/P,leukocyte elastase,Trypsin,proline endopeptidase,Alpha-lytic protease,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
SimpleSearchEngine	-	Search:enzyme	string	Trypsin	Trypsin,Arg-C,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Arg-C/P,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
SiriusAdapter	+	preprocessing:precursor_mz_tolerance	double	5.0e-03		
SiriusAdapter	-	preprocessing:precursor_mz_tolerance	double	0.005		
SpectraSTSearchAdapter	+	output_files	output-file			*.txt,*.tsv,*.xml,*.pepXML,*.html
SpectraSTSearchAdapter	+	spectra_files	input-file			*.mzML,*.mzXML,*.mzData,*.mgf,*.dta,*.msp
SpectraSTSearchAdapter	-	output_files	output-file			*.txt,*.tsv,*.pep.xml,*.xml,*.pepXML,*.html
SpectraSTSearchAdapter	-	spectra_files	input-file			*.mzML,*.mzXML,*.mzData,*.dta,*.msp
TOFCalibration	+	algorithm:PeakPicker:wavelet_transform:spacing	double	1.0e-03	0.0:	
TOFCalibration	+	ref_masses	input-file			*.txt,*.tsv
TOFCalibration	+	tof_const	input-file			*.tsv
TOFCalibration	-	algorithm:PeakPicker:wavelet_transform:spacing	double	0.001	0.0:	
TOFCalibration	-	ref_masses	input-file			*.txt
TOFCalibration	-	tof_const	input-file			*.csv
TextExporter	+	out	output-file			*.tsv
TextExporter	-	out	output-file			*.csv
TransformationEvaluation	+	step	double	1.0	1.0e-03:	
TransformationEvaluation	-	step	double	1.0	0.001:	
XMLValidator	+	in	input-file			*.mzML,*.mzData,*.featureXML,*.mzid,*.idXML,*.consensusXML,*.mzXML,*.ini,*.pepXML,*.traML,*.xml
XMLValidator	-	in	input-file			*.mzML,*.mzData,*.featureXML,*.mzid,*.idXML,*.consensusXML,*.mzXML,*.ini,*.pepXML,*.TraML,*.xml
XTandemAdapter	+	enzyme	string	Trypsin	Alpha-lytic protease,V8-E,glutamyl endopeptidase,2-iodobenzoate,unspecific cleavage,leukocyte elastase,Arg-C/P,Trypsin,Arg-C,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P	
XTandemAdapter	-	enzyme	string	Trypsin	Arg-C,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,unspecific cleavage,Asp-N/B,Asp-N,Asp-N_ambic,Trypsin,Arg-C/P	
