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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit 44c3e37a12f60b01521d3e3f18b7f16664f954cc"
author galaxyp
date Tue, 07 Apr 2020 03:27:32 -0400
parents d796e6613d19
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d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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1 # Hardklor parameter file
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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2 # Version 2.3.0
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3 # Please see online documentation for detailed explanations:
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4 # https://code.google.com/p/hardklor/wiki/Documentation
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d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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6 # All parameters are separated from their values by an equals sign ('=')
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7 # Anything after a '#' will be ignored for the remainder of the line.
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8 # All data files (including paths if necessary) to be analyzed are discussed below.
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d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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10 # Parameters used to described the data being input to Hardklor
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11 instrument = {instrument} #Values are: FTICR, Orbitrap, TOF, QIT
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12 resolution = {resolution} #Resolution at 400 m/z (def. 60000)
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13 centroided = {centroided} #0=no, 1=yes
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15 # Parameters used in preprocessing spectra prior to analysis
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16 ms_level = {mslvl} #1=MS1, 2=MS2, 3=MS3, 0=all
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17 scan_range_min = 0 #ignore any spectra lower than this number, 0=off
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18 scan_range_max = 0 #ignore any spectra higher than this number, 0=off
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19 signal_to_noise = 0 #set signal-to-noise ratio, 0=off
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20 sn_window = 250.0 #size in m/z for computing localized noise level in a spectrum.
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21 static_sn = 0 #0=off, 1=on. Apply lowest localized noise level to entire spectrum.
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22 boxcar_averaging = 0 #0=off, or specify number of scans to average together, use odd numbers only
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23 boxcar_filter = 0 #0=off, when using boxcar_averaging, only keep peaks seen in this number of scans
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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24 # currently being averaged together. When on, signal_to_noise is not used.
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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25 boxcar_filter_ppm = 5 #Tolerance in ppm for matching peaks across spectra in boxcar_filter
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26 mz_min = 0 #Sets lower bound of spectrum m/z range to analyze, 0=off
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27 mz_max = 0 #Sets upper bound of spectrum m/z range to analyze, 0=off
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28 smooth = 0 #Peforms Savitzky-Golay smoothing of peaks data. 0=off
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29 # Not recommended for high resolution data.
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31 # Parameters used to customize the Hardklor analysis. Some of these parameters will drastically
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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32 # affect the analysis speed and results. Please consult the documentation and choose carefully!
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33 algorithm = {algorithm} #Algorithms include: Basic, Version1, Version2
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34 charge_algorithm = {charge_algo} #Preferred method for feature charge identification.
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35 # Values are: Quick, FFT, Patterson, Senko, None
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36 # If None is set, all charge states are assumed, slowing Hardklor
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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37 charge_min = {mincharge} #Lowest charge state allowed in the analysis.
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38 charge_max = {maxcharge} #Highest charge state allowed in the analysis.
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39 correlation = {correlation} #Correlation threshold to accept a peptide feature.
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40 averagine_mod = 0 #Formula containing modifications to the averagine model.
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41 # Read documentation carefully before using! 0=off
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42 mz_window = 5.25 #Breaks spectrum into windows not larger than this value for Version1 algorithm.
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43 sensitivity = {sensitivity} #Values are 0 (lowest) to 3 (highest). Increasing sensitivity
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44 # identifies more features near the noise where the isotope distribution
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45 # may not be fully visible. However, these features are also more
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46 # likely to be false.
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47 depth = {depth} #Depth of combinatorial analysis. This is the maximum number of overlapping
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48 # features allowed in any mz_window. Each increase requires exponential
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49 # computation. In other words, keep this as low as necessary!!!
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50 max_features = {maxfeat} #Maximum number of potential features in an mz_window to combinatorially solve.
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51 # Setting this too high results in wasted computation time trying to mix-and-match
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52 # highly improbable features.
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53
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54 # Parameters used to customize the Hardklor output
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55 distribution_area = 1 #Report sum of distribution peaks instead of highest peak only. 0=off, 1=on
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56 xml = 0 #Output results as XML. 0=off, 1=on
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57
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59 # Below this point is where files to be analyzed should go. They should be listed contain
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60 # both the input file name, and the output file name. Each file to be analyzed should begin
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61 # on a new line. By convention Hardklor output should have this extension: .hk
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62 # Example:
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63 #YourData.mzXML YourData.hk
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64 #Data.mzXML Data.hk
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65 {inputfile} {outputfile}