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comparison hardklor.conf @ 0:d796e6613d19 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
author galaxyp
date Mon, 23 May 2016 11:12:40 -0400
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1 # Hardklor parameter file
2 # Version 2.3.0
3 # Please see online documentation for detailed explanations:
4 # https://code.google.com/p/hardklor/wiki/Documentation
5
6 # All parameters are separated from their values by an equals sign ('=')
7 # Anything after a '#' will be ignored for the remainder of the line.
8 # All data files (including paths if necessary) to be analyzed are discussed below.
9
10 # Parameters used to described the data being input to Hardklor
11 instrument = {instrument} #Values are: FTICR, Orbitrap, TOF, QIT
12 resolution = {resolution} #Resolution at 400 m/z (def. 60000)
13 centroided = {centroided} #0=no, 1=yes
14
15 # Parameters used in preprocessing spectra prior to analysis
16 ms_level = {mslvl} #1=MS1, 2=MS2, 3=MS3, 0=all
17 scan_range_min = 0 #ignore any spectra lower than this number, 0=off
18 scan_range_max = 0 #ignore any spectra higher than this number, 0=off
19 signal_to_noise = 0 #set signal-to-noise ratio, 0=off
20 sn_window = 250.0 #size in m/z for computing localized noise level in a spectrum.
21 static_sn = 0 #0=off, 1=on. Apply lowest localized noise level to entire spectrum.
22 boxcar_averaging = 0 #0=off, or specify number of scans to average together, use odd numbers only
23 boxcar_filter = 0 #0=off, when using boxcar_averaging, only keep peaks seen in this number of scans
24 # currently being averaged together. When on, signal_to_noise is not used.
25 boxcar_filter_ppm = 5 #Tolerance in ppm for matching peaks across spectra in boxcar_filter
26 mz_min = 0 #Sets lower bound of spectrum m/z range to analyze, 0=off
27 mz_max = 0 #Sets upper bound of spectrum m/z range to analyze, 0=off
28 smooth = 0 #Peforms Savitzky-Golay smoothing of peaks data. 0=off
29 # Not recommended for high resolution data.
30
31 # Parameters used to customize the Hardklor analysis. Some of these parameters will drastically
32 # affect the analysis speed and results. Please consult the documentation and choose carefully!
33 algorithm = {algorithm} #Algorithms include: Basic, Version1, Version2
34 charge_algorithm = {charge_algo} #Preferred method for feature charge identification.
35 # Values are: Quick, FFT, Patterson, Senko, None
36 # If None is set, all charge states are assumed, slowing Hardklor
37 charge_min = {mincharge} #Lowest charge state allowed in the analysis.
38 charge_max = {maxcharge} #Highest charge state allowed in the analysis.
39 correlation = {correlation} #Correlation threshold to accept a peptide feature.
40 averagine_mod = 0 #Formula containing modifications to the averagine model.
41 # Read documentation carefully before using! 0=off
42 mz_window = 5.25 #Breaks spectrum into windows not larger than this value for Version1 algorithm.
43 sensitivity = {sensitivity} #Values are 0 (lowest) to 3 (highest). Increasing sensitivity
44 # identifies more features near the noise where the isotope distribution
45 # may not be fully visible. However, these features are also more
46 # likely to be false.
47 depth = {depth} #Depth of combinatorial analysis. This is the maximum number of overlapping
48 # features allowed in any mz_window. Each increase requires exponential
49 # computation. In other words, keep this as low as necessary!!!
50 max_features = {maxfeat} #Maximum number of potential features in an mz_window to combinatorially solve.
51 # Setting this too high results in wasted computation time trying to mix-and-match
52 # highly improbable features.
53
54 # Parameters used to customize the Hardklor output
55 distribution_area = 1 #Report sum of distribution peaks instead of highest peak only. 0=off, 1=on
56 xml = 0 #Output results as XML. 0=off, 1=on
57
58
59 # Below this point is where files to be analyzed should go. They should be listed contain
60 # both the input file name, and the output file name. Each file to be analyzed should begin
61 # on a new line. By convention Hardklor output should have this extension: .hk
62 # Example:
63 #YourData.mzXML YourData.hk
64 #Data.mzXML Data.hk
65 {inputfile} {outputfile}