ZNova Command Line Options Reference

Parameter strings or command line switches can control many of the ZNova Parameters.  The command line arguments are used in the ZNova Params field of the Xcalibur Sequence Setup view to specify deconvolution options. ZNova-ize Sequence will add parameter strings to an Xcalibur Sequence for you automatically. Therefore, there is really no need to know these options for everyday use. However, you may find the command line arguments to be helpful if you want to write your own scripts to automate ZNova in special applications (e.g., a CGI application), or if you want to save time and enter them directly in Xcalibur sample list.  Please note that the command line options are case sensitive. Examples given below are shown in the context of running the ZNova deconvolution from the command line (i.e., from a windows console or command prompt) or from the Xcalibur sample list.

 Specifying a plain text file for input

command line option: -d "datafile"

command line example: xznova -d “c:\mydata\myoglobin.txt”

sample list example: N/A

  Specifying an ProMass text file for input

command line option: -X "datafile"

command line example: xznova -X “c:\xcalibur\data\myolcms.txt”

sample list example: N/A

 Specifying a clipboard spectrum for input

command line option: -C

command line example: xznova -C

sample list example: N/A

 Specifying a parameter file

command line option: -P "parameterFile"

command line example: xznova -X “c:\xcalibur\data\myolcms.txt” -P “c:\promassxcali\znova\znova.params”

sample list example:  -P “c:\promassxcali\znova\znova.params”

 Specifying an explicit results directory .

command line option: -D "resultsDirectory"

command line example: xznova -X “c:\xcalibur\data\myolcms.txt” -D “c:\Xcalibur\data\my_results”

sample list example:  -D “c:\Xcalibur\data\my_results”

 Adduct Ion Mass (sets the numeric value of the mass of the adduct ion)

command line option: -a mass

command line example: xznova -d “c:\mydata\oligo.txt” -a -1.0079

sample list example:   -a -1.0079

 Comprehensive Deconvolution Mode, ON  (turns ON comprehensive decon mode)

command line option: -x

command line example: xznova -d “c:\mydata\myoglobin.txt” -x

sample list example:   -x

 Comprehensive Deconvolution Mode, OFF  (turns OFF comprehensive decon mode)

command line option: -y

command line example: xznova -d “c:\mydata\myoglobin.txt” -y

sample list example:   -y

 Peak Width (sets the numeric value for input peak width)

command line option: -p pw

command line example: xznova -d “c:\mydata\bighairyprotein.txt” -p 5

sample list example:   -p 5

 Merge Width (sets the numeric value for merge width)

command line option: -m merge

command line example: xznova -d “c:\mydata\bighairyprotein.txt” -p 5 -m 0.3

sample list example:   -p 5 -m 0.3 

 Normalize Scores (sets the numeric value for the charge state where score normalization begins)

command line option: -n charge

example: xznova -d “c:\mydata\peptide.txt” -p 2 -n 3

sample list example: -p 2 -n 3 

 Minimum Score (sets the numeric value of the minimum score)

command line option: -s score

command line example: xznova -d “c:\mydata\bighairyprotein.txt” -s 3

sample list example: -s 3

 First m/z (sets the numeric value for the first m/z in the input data set)

command line option: -f mz

command line example: xznova -d “c:\mydata\peptide.txt” -f 700 -l 1500

sample list example: -f 700 -l 1500 

Last m/z (sets the numeric value for the last m/z in the input data set)

command line option: -l mz

command line example: xznova -d “c:\mydata\peptide.txt” -f 700 -l 1500

sample list example: -f 700 -l 1500 

 Minimum Mass (sets the numeric value for the minimum deconvoluted mass)

command line option: -F mass

command line example: xznova -d “c:\mydata\protein.txt” -f 700 -l 1500 -F 5000 -L 30000

sample list example: -f 700 -l 1500 -F 5000 -L 30000

 Maximum Mass (sets the numeric value for the maximum deconvoluted mass)

command line option: -L mass

command line example: xznova -d “c:\mydata\protein.txt” -f 700 -l 1500 -F 5000 -L 30000

sample list example: -f 700 -l 1500 -F 5000 -L 30000 

 Smooth Width (sets the numeric value for the smooth width)

command line option: -w sw

command line example: xznova -d “c:\mydata\bighairyprotein.txt” -w 5

sample list example: -w 5

 Noise threshold % (sets the numeric value for the %relative intensity noise threshold, setting this option to 0 sets noise thresholding to auto mode)

command line option: -t thresh

command line example: xznova -d “c:\mydata\bighairyprotein.txt” -t 10

sample list example: -t 10

 Signal-to-noise threshold (sets the numeric value for automatic S/N thresholding, default = 2)

command line option: -S thresh

command line example: xznova -d “c:\mydata\bighairyprotein.txt” -S 3

sample list example: -S 3

 Baseline Factor (sets the numeric value of the baseline removal factor)

command line option: -b base

command line example: xznova -d “c:\mydata\bighairyprotein.txt” -b 1.2

sample list example: -b 1.2 

 Maximum Components (sets the numeric value for the maximum number of found components, has no effect in comprehensive decon mode)

command line option: -c comp

command line example: xznova -d “c:\mydata\bighairyprotein.txt” -c 5

sample list example: -c 5

 Maximum Iterations (sets the numeric value for the maximum number of znova iterations, has no effect in comprehensive decon mode)

command line option: -i iter

command line example: xznova -d “c:\mydata\bighairyprotein.txt” -i 100

sample list example: -i 100

 Maximum Time (sets the numeric value for the maximum znova algorithm dead time in seconds)

command line option: -e time

command line example: xznova -d “c:\mydata\bighairyprotein.txt” -e 60

sample list example: -e 60