Crux parameters

 assign-confidencecascade-searchcometcomet-indexcreate-docsbullseyehardklorgenerate-peptidesget-ms2-spectrumkojakmake-pinlocalize-modificationparam-medicpercolatorpipelinepredict-peptide-ionsprint-processed-spectrapsm-convertread-tide-indexspectral-countssubtract-indextide-indextide-searchdiameterspectrum-converter
estimation-method                      
decoy-prefix                  
score                      
sidak                      
top-match-in                      
verbosity   
parameter-file     
overwrite    
output-dir     
list-of-files                      
combine-charge-states                      
combine-modified-peptides                      
fileroot          
q-value-threshold                        
auto-mz-bin-width                      
auto-precursor-window                      
concat                      
deisotope                      
fragment-tolerance                      
isotope-error                      
mass-precision                    
max-precursor-charge                     
min-precursor-charge                      
min-peaks                      
mod-precision                   
mz-bin-offset                     
mz-bin-width                     
mzid-output                     
mztab-output                      
num-threads                     
override-charges                      
pepxml-output                      
pin-output                      
pm-charges                  
pm-max-frag-mz                  
pm-max-precursor-delta-ppm                  
pm-max-precursor-mz                  
pm-max-scan-separation                  
pm-min-common-frag-peaks                  
pm-min-frag-mz                  
pm-min-peak-pairs                  
pm-min-precursor-mz                  
pm-min-scan-frag-peaks                  
pm-pair-top-n-frag-peaks                  
pm-top-n-frag-peaks                  
precision                      
precursor-window                      
precursor-window-type                      
print-search-progress                      
remove-precursor-peak                      
remove-precursor-tolerance                     
scan-number                     
score-function                      
skip-preprocessing                      
spectrum-max-mz                      
spectrum-min-mz                      
spectrum-parser                  
sqt-output                      
store-index                      
store-spectra                      
txt-output                     
use-flanking-peaks                      
use-neutral-loss-peaks                      
use-z-line                    
decoy_search                      
peff_format                      
peff_obo                      
num_threads                      
peptide_mass_tolerance                      
auto_peptide_mass_tolerance                      
peptide_mass_units                      
mass_type_parent                      
mass_type_fragment                      
precursor_tolerance_type                      
isotope_error                      
search_enzyme_number                      
search_enzyme2_number                      
num_enzyme_termini                      
allowed_missed_cleavage                      
fragment_bin_tol                      
fragment_bin_offset                     
auto_fragment_bin_tol                      
theoretical_fragment_ions                      
use_A_ions                      
use_B_ions                      
use_C_ions                      
use_X_ions                      
use_Y_ions                      
use_Z_ions                      
use_Z1_ions                      
use_NL_ions                      
output_mzidentmlfile                      
output_pepxmlfile                      
output_percolatorfile                      
output_sqtfile                      
output_sqtstream                      
output_txtfile                      
print_expect_score                      
num_output_lines                      
show_fragment_ions                      
sample_enzyme_number                      
scan_range                      
precursor_charge                      
override_charge                      
ms_level                      
activation_method                      
clip_nterm_methionine                      
decoy_prefix                      
digest_mass_range                      
equal_I_and_L                      
mass_offsets                      
max_duplicate_proteins                      
max_fragment_charge                      
max_index_runtime                      
max_precursor_charge                      
num_results                      
nucleotide_reading_frame                      
output_suffix                      
peptide_length_range                      
precursor_NL_ions                      
skip_researching                      
spectrum_batch_size                      
text_file_extension                      
explicit_deltacn                      
old_mods_encoding                      
minimum_peaks                      
minimum_intensity                      
remove_precursor_peak                      
remove_precursor_tolerance                      
clear_mz_range                      
variable_mod01                      
variable_mod02                      
variable_mod03                      
variable_mod04                      
variable_mod05                      
variable_mod06                      
variable_mod07                      
variable_mod08                      
variable_mod09                      
auto_modifications                      
max_variable_mods_in_peptide                      
require_variable_mod                      
protein_modlist_file                      
add_Cterm_peptide                      
add_Nterm_peptide                      
add_Cterm_protein                      
add_Nterm_protein                      
add_A_alanine                      
add_C_cysteine                      
add_D_aspartic_acid                      
add_E_glutamic_acid                      
add_F_phenylalanine                      
add_G_glycine                      
add_H_histidine                      
add_I_isoleucine                      
add_K_lysine                      
add_L_leucine                      
add_M_methionine                      
add_N_asparagine                      
add_O_pyrrolysine                      
add_P_proline                      
add_Q_glutamine                      
add_R_arginine                      
add_S_serine                      
add_T_threonine                      
add_U_selenocysteine                      
add_V_valine                      
add_W_tryptophan                      
add_Y_tyrosine                      
add_B_user_amino_acid                      
add_J_user_amino_acid                      
add_X_user_amino_acid                      
add_Z_user_amino_acid                      
fragindex_skipreadprecursors                      
fragindex_num_spectrumpeaks                      
fragindex_min_ions_score                      
fragindex_min_ions_report                      
fragindex_min_fragmentmass                      
fragindex_max_fragmentmass                      
create_peptide_index                        
max-persist                       
exact-match                       
exact-tolerance                       
persist-tolerance                       
gap-tolerance                       
scan-tolerance                       
bullseye-max-mass                       
bullseye-min-mass                       
retention-tolerance                       
spectrum-format                       
hardklor-algorithm                        
averagine-mod                        
boxcar-averaging                        
boxcar-filter                        
boxcar-filter-ppm                        
centroided                        
cdm                        
min-charge                        
max-charge                        
corr                        
depth                        
distribution-area                        
hardklor-data-file                        
instrument                        
isotope-data-file                        
max-features                        
mzxml-filter                        
mz-max                        
mz-min                        
mz-window                        
resolution                        
scan-range-max                        
scan-range-min                        
sensitivity                        
signal-to-noise                        
smooth                        
sn-window                        
static-sn                        
min-mass                      
max-mass                      
min-length                      
max-length                      
enzyme                      
custom-enzyme                      
digestion                      
missed-cleavages                      
isotopic-mass                      
seed                      
clip-nterm-methionine                      
decoy-format                      
keep-terminal-aminos                      
stats                        
threads                        
export_percolator                        
export_mzID                        
export_pepXML                        
enrichment                        
MS1_centroid                        
MS2_centroid                        
MS1_resolution                        
MS2_resolution                        
cross_link                        
mono_link                        
fixed_modification                        
fixed_modification_protC                        
fixed_modification_protN                        
modification                        
modification_protC                        
modification_protN                        
diff_mods_on_xl                        
max_mods_per_peptide                        
mono_links_on_xl                        
fragment_bin_size                        
auto_fragment_bin_size                        
ion_series_A                        
ion_series_B                        
ion_series_C                        
ion_series_X                        
ion_series_Y                        
ion_series_Z                        
decoy_filter                        
max_miscleavages                        
max_peptide_mass                        
min_peptide_mass                        
min_peptide_score                        
min_spectrum_peaks                        
max_spectrum_peaks                        
ppm_tolerance_pre                        
auto_ppm_tolerance_pre                        
precursor_refinement                        
prefer_precursor_pred                        
spectrum_processing                        
top_count                        
e_value_depth                        
truncate_prot_names                        
kojak_instrument                        
kojak_enzyme                        
kojak_isotope_error                        
max-charge-feature                      
output-file                        
top-match                   
unique-scannr                        
min-mod-mass                        
c-neg                       
c-pos                       
decoy-xml-output                       
default-direction                       
feature-file-out                       
fido-alpha                       
fido-beta                       
fido-empirical-protein-q                       
fido-fast-gridsearch                       
fido-gamma                       
fido-gridsearch-depth                       
fido-gridsearch-mse-threshold                       
fido-no-split-large-components                       
fido-protein-truncation-threshold                       
init-weights                       
klammer                       
maxiter                       
no-terminate                       
only-psms                       
output-weights                       
override                       
percolator-seed                       
picked-protein                       
pout-output                       
protein                       
protein-enzyme                       
protein-report-duplicates                       
protein-report-fragments                       
protein-name-separator                       
quick-validation                       
search-input                       
spectral-counting-fdr                       
static                       
subset-max-train                       
tdc                       
test-each-iteration                       
test-fdr                       
train-best-positive                       
train-fdr                       
unitnorm                       
bullseye                        
search-engine                        
post-processor                        
allow-dups                       
cterm-peptide-mods-spec                       
cterm-protein-mods-spec                       
max-mods                       
memory-limit                       
min-mods                       
mods-spec                       
nterm-peptide-mods-spec                       
nterm-protein-mods-spec                       
auto-modifications                       
auto-modifications-spectra                       
num-decoys-per-target                       
peptide-list                      
temp-dir                       
parsimony                       
threshold                       
threshold-type                       
input-ms2                       
unique-mapping                       
quant-level                       
measure                       
custom-threshold-name                       
custom-threshold-min                       
mzid-use-pass-threshold                       
protein-database                      
primary-ions                        
precursor-ions                        
isotope                        
flanking                        
max-ion-charge                        
fragment-mass                        
nh3                        
h2o                        
stop-after                        
output-units                        
input-format                        
distinct-matches                        
predrt-files                        
prec-ppm                        
frag-ppm                        
diameter-instrument                        
spectrum-outdir