Crux parameters

 assign-confidencecascade-searchcometcreate-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                      
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                      
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