# Hardklor parameter file
# Version 2.3.0
# Please see online documentation for detailed explanations: 
# https://code.google.com/p/hardklor/wiki/Documentation

# All parameters are separated from their values by an equals sign ('=')
# Anything after a '#' will be ignored for the remainder of the line.
# All data files (including paths if necessary) to be analyzed are discussed below.

# Parameters used to described the data being input to Hardklor
instrument	=	{instrument} #Values are: FTICR, Orbitrap, TOF, QIT
resolution	=	{resolution} #Resolution at 400 m/z (def. 60000)	
centroided	=	{centroided}   #0=no, 1=yes

# Parameters used in preprocessing spectra prior to analysis
ms_level			=	{mslvl}		#1=MS1, 2=MS2, 3=MS3, 0=all
scan_range_min		=	0		#ignore any spectra lower than this number, 0=off
scan_range_max		=	0		#ignore any spectra higher than this number, 0=off
signal_to_noise		=	0		#set signal-to-noise ratio, 0=off
sn_window			=	250.0	#size in m/z for computing localized noise level in a spectrum.
static_sn			=	0		#0=off, 1=on. Apply lowest localized noise level to entire spectrum.
boxcar_averaging	=	0		#0=off, or specify number of scans to average together, use odd numbers only
boxcar_filter		=	0		#0=off, when using boxcar_averaging, only keep peaks seen in this number of scans
								#  currently being averaged together. When on, signal_to_noise is not used.
boxcar_filter_ppm	=	5		#Tolerance in ppm for matching peaks across spectra in boxcar_filter
mz_min				=	0		#Sets lower bound of spectrum m/z range to analyze, 0=off
mz_max				=	0		#Sets upper bound of spectrum m/z range to analyze, 0=off
smooth				=	0		#Peforms Savitzky-Golay smoothing of peaks data. 0=off
								#  Not recommended for high resolution data.

# Parameters used to customize the Hardklor analysis. Some of these parameters will drastically
# affect the analysis speed and results. Please consult the documentation and choose carefully!
algorithm			=	{algorithm} #Algorithms include: Basic, Version1, Version2
charge_algorithm	=	{charge_algo} #Preferred method for feature charge identification.
									#  Values are: Quick, FFT, Patterson, Senko, None
									#  If None is set, all charge states are assumed, slowing Hardklor
charge_min			=	{mincharge}			#Lowest charge state allowed in the analysis.
charge_max			=	{maxcharge}			#Highest charge state allowed in the analysis.
correlation			=	{correlation}		#Correlation threshold to accept a peptide feature.
averagine_mod		=	0			#Formula containing modifications to the averagine model.
									#  Read documentation carefully before using! 0=off
mz_window			=	5.25		#Breaks spectrum into windows not larger than this value for Version1 algorithm.
sensitivity			=	{sensitivity}			#Values are 0 (lowest) to 3 (highest). Increasing sensitivity
									#  identifies more features near the noise where the isotope distribution
									#  may not be fully visible. However, these features are also more
									#  likely to be false.
depth				=	{depth}			#Depth of combinatorial analysis. This is the maximum number of overlapping
									#  features allowed in any mz_window. Each increase requires exponential
									#  computation. In other words, keep this as low as necessary!!!
max_features		=	{maxfeat}			#Maximum number of potential features in an mz_window to combinatorially solve.
									#  Setting this too high results in wasted computation time trying to mix-and-match
									#  highly improbable features.

# Parameters used to customize the Hardklor output
distribution_area	=	1	#Report sum of distribution peaks instead of highest peak only. 0=off, 1=on
xml					=	0	#Output results as XML. 0=off, 1=on


# Below this point is where files to be analyzed should go. They should be listed contain 
# both the input file name, and the output file name. Each file to be analyzed should begin 
# on a new line. By convention Hardklor output should have this extension: .hk
# Example:
#YourData.mzXML YourData.hk
#Data.mzXML Data.hk
{inputfile} {outputfile}
