Crux parameters

 assign-confidencebaristacascade-searchcometcreate-docsbullseyehardklorextract-columnsextract-rowsgenerate-peptidesget-ms2-spectrummake-pinlocalize-modificationparam-medicpercolatorpipelinepredict-peptide-ionsprint-processed-spectrapsm-convertq-rankerread-tide-indexsearch-for-xlinkssort-by-columnspectral-countsstat-columnsubtract-indextide-indextide-searchxlink-assign-ionsxlink-score-spectrum
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                 
enzyme                         
separate-searches                            
pepxml-output                        
txt-output                        
skip-cleanup                            
re-run                            
use-spec-features                            
feature-file-out                          
optimization                             
spectrum-parser                   
q-value-threshold                             
auto-mz-bin-width                           
auto-precursor-window                           
compute-sp                          
concat                          
deisotope                           
exact-p-value                           
file-column                          
isotope-error                           
mass-precision                         
max-precursor-charge                           
min-peaks                           
mod-precision                       
mz-bin-offset                          
mz-bin-width                         
mzid-output                          
num-threads                           
peptide-centric-search                           
score-function                           
fragment-tolerance                           
evidence-granularity                           
pin-output                           
pm-charge                         
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                         
skip-preprocessing                           
spectrum-charge                          
spectrum-max-mz                          
spectrum-min-mz                          
sqt-output                           
store-index                           
store-spectra                           
use-flanking-peaks                         
use-neutral-loss-peaks                           
use-z-line                        
decoy_search                            
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                            
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_NL_ions                            
output_sqtfile                            
output_txtfile                            
output_pepxmlfile                            
output_percolatorfile                            
output_outfiles                            
print_expect_score                            
num_output_lines                            
show_fragment_ions                            
sample_enzyme_number                            
scan_range                            
precursor_charge                            
override_charge                            
ms_level                            
activation_method                            
digest_mass_range                            
num_results                            
skip_researching                            
max_fragment_charge                            
max_precursor_charge                            
nucleotide_reading_frame                            
clip_nterm_methionine                            
spectrum_batch_size                            
decoy_prefix                            
output_suffix                            
mass_offsets                            
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                            
max_variable_mods_in_peptide                            
require_variable_mod                            
add_Cterm_peptide                            
add_Nterm_peptide                            
add_Cterm_protein                            
add_Nterm_protein                            
add_A_alanine                            
add_B_user_amino_acid                            
add_C_cysteine                            
add_D_aspartic_acid                            
add_E_glutamic_acid                            
add_F_phenylalanine                            
add_G_glycine                            
add_H_histidine                            
add_I_isoleucine                            
add_J_user_amino_acid                            
add_K_lysine                            
add_L_leucine                            
add_M_methionine                            
add_N_asparagine                            
add_O_ornithine                            
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_X_user_amino_acid                            
add_Y_tyrosine                            
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                             
delimiter                          
header                          
comparison                             
column-type                            
min-mass                           
max-mass                           
min-length                           
max-length                           
custom-enzyme                           
digestion                           
missed-cleavages                           
isotopic-mass                           
seed                           
clip-nterm-methionine                            
decoy-format                            
keep-terminal-aminos                            
stats                             
max-charge-feature                           
output-file                             
top-match                        
min-mod-mass                             
c-neg                            
c-pos                            
decoy-xml-output                            
default-direction                            
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                            
only-psms                            
output-weights                            
override                            
percolator-seed                            
picked-protein                            
pout-output                            
protein                            
protein-enzyme                            
protein-report-duplicates                            
protein-report-fragments                            
quick-validation                            
search-input                            
spectral-counting-fdr                            
subset-max-train                            
tdc                            
test-each-iteration                            
test-fdr                            
train-best-positive                            
train-fdr                            
unitnorm                            
bullseye                             
search-engine                             
post-processor                             
primary-ions                             
precursor-ions                             
isotope                             
flanking                             
max-ion-charge                           
fragment-mass                           
nh3                             
h2o                             
stop-after                             
output-units                             
input-format                             
distinct-matches                             
protein-database                            
use-old-xlink                             
xlink-include-linears                             
xlink-include-deadends                             
xlink-include-selfloops                             
xlink-include-inter                             
xlink-include-intra                             
xlink-include-inter-intra                             
xlink-prevents-cleavage                             
require-xlink-candidate                             
xlink-top-n                             
max-xlink-mods                             
mods-spec                            
cmod                             
nmod                             
max-mods                            
mono-link                             
precursor-window-weibull                             
precursor-window-type-weibull                             
min-weibull-points                             
use-a-ions                            
use-b-ions                            
use-c-ions                            
use-x-ions                            
use-y-ions                            
use-z-ions                            
mod-mass-format                             
isotope-windows                             
compute-p-values                             
ascending                             
parsimony                             
threshold                             
threshold-type                             
input-ms2                             
unique-mapping                             
quant-level                             
measure                             
custom-threshold-name                             
custom-threshold-min                             
mzid-use-pass-threshold                             
peptide-list                            
allow-dups                             
cterm-peptide-mods-spec                             
min-mods                             
nterm-peptide-mods-spec                             
num-decoys-per-target                             
temp-dir                             
xlink-score-method