Mercurial > repos > computational-metabolomics > mspurity_combineannotations

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
author computational-metabolomics
date Wed, 12 Jun 2024 16:06:42 +0000
parents 18c0038dde9c
children f11c129a4227
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7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
1 library(msPurity)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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2 library(optparse)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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3 print(sessionInfo())
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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4 option_list <- list(
8
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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5 make_option(c("-o", "--out_dir"),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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6 type = "character", default = getwd(),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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7 help = "Output folder for resulting files [default = %default]"
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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8 ),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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9 make_option(c("-x", "--xset_path"),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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10 type = "character", default = file.path(getwd(), "xset.rds"),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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11 help = "The path to the xcmsSet object [default = %default]"
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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12 ),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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13 make_option("--polarity",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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14 default = NA,
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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15 help = "polarity (just used for naming purpose for files being saved) [positive, negative, NA] [default %default]"
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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16 ),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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17 make_option("--rsd_i_blank",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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18 default = 100,
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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19 help = "RSD threshold for the blank [default = %default]"
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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20 ),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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21 make_option("--minfrac_blank",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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22 default = 0.5,
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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23 help = "minimum fraction of files for features needed for the blank [default = %default]"
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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24 ),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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25 make_option("--rsd_rt_blank",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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26 default = 100,
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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27 help = "RSD threshold for the RT of the blank [default = %default]"
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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28 ),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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29 make_option("--ithres_blank",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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30 default = 0,
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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31 help = "Intensity threshold for the blank [default = %default]"
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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32 ),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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33 make_option("--s2b",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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34 default = 10,
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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35 help = "fold change (sample/blank) needed for sample peak to be allowed. e.g.
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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36 if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10.
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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37 1000/10 = 100, so sample has fold change higher than the threshold and the peak
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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38 is not considered a blank [default = %default]"
8
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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39 ),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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40 make_option("--blank_class",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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41 default = "blank", type = "character",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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42 help = "A string representing the class that will be used for the blank.[default = %default]"
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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43 ),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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44 make_option("--egauss_thr",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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45 default = NA,
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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46 help = "Threshold for filtering out non gaussian shaped peaks. Note this only works
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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47 if the 'verbose columns' and 'fit gauss' was used with xcms
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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48 [default = %default]"
8
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49 ),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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50 make_option("--rsd_i_sample",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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51 default = 100,
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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52 help = "RSD threshold for the samples [default = %default]"
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53 ),
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54 make_option("--minfrac_sample",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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55 default = 0.8,
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56 help = "minimum fraction of files for features needed for the samples [default = %default]"
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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57 ),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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58 make_option("--rsd_rt_sample",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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59 default = 100,
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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60 help = "RSD threshold for the RT of the samples [default = %default]"
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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61 ),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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62 make_option("--ithres_sample",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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63 default = 5000,
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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64 help = "Intensity threshold for the sample [default = %default]"
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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65 ),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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66 make_option("--grp_rm_ids",
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67 default = NA,
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68 help = "vector of grouped_xcms peaks to remove (corresponds to the row from xcms::group output)
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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69 [default = %default]"
8
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70 ),
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71 make_option("--remove_spectra",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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72 action = "store_true",
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73 help = "TRUE if flagged spectra is to be removed [default = %default]"
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74 ),
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75 make_option("--minfrac_xcms",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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76 default = 0.5,
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77 help = "minfrac for xcms grouping [default = %default]"
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78 ),
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79 make_option("--mzwid",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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80 default = 0.001,
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81 help = "mzwid for xcms grouping [default = %default]"
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82 ),
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83 make_option("--bw",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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84 default = 5,
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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85 help = "bw for xcms grouping [default = %default]"
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86 ),
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87 make_option("--temp_save",
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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88 action = "store_true",
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89 help = "Assign True if files for each step saved (for testing purposes) [default = %default]"
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90 ),
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91 make_option("--samplelist", type = "character", help = "Sample list to determine the blank class")
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92 )
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93
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94 # nolint start
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95 # make_option("--multilist", action="store_true"
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96 # help="NOT CURRENTLY IMPLEMENTED: If paired blank removal is to be performed a - multilist - sample list file has to be provided"
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97 # ),
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98 # nolint end
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99
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100 # store options
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101 opt <- parse_args(OptionParser(option_list = option_list))
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102
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103 opt <- replace(opt, opt == "NA", NA)
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104
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105 if (is.null(opt$temp_save)) {
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106 temp_save <- FALSE
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107 } else {
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108 temp_save <- TRUE
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109 }
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110
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111 if (is.null(opt$remove_spectra)) {
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112 remove_spectra <- FALSE
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113 } else {
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114 remove_spectra <- TRUE
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115 }
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116
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117
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118 print(opt)
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119
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120 getxcmsSetObject <- function(xobject) {
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121 # XCMS 1.x
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122 if (class(xobject) == "xcmsSet") {
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123 return(xobject)
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124 }
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125 # XCMS 3.x
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126 if (class(xobject) == "XCMSnExp") {
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127 # Get the legacy xcmsSet object
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128 suppressWarnings(xset <- as(xobject, "xcmsSet"))
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129 xcms::sampclass(xset) <- xset@phenoData$sample_group
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130 return(xset)
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131 }
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132 }
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133
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134
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135 loadRData <- function(rdata_path, name) {
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136 # loads an RData file, and returns the named xset object if it is there
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137 load(rdata_path)
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138 return(get(ls()[ls() %in% name]))
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139 }
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140
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141 xset <- getxcmsSetObject(loadRData(opt$xset_path, c("xset", "xdata")))
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142
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143 print(xset)
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144 if (is.null(opt$samplelist)) {
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145 blank_class <- opt$blank_class
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146 } else {
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147 samplelist <- read.table(opt$samplelist, sep = "\t", header = TRUE)
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148 samplelist_blank <- unique(samplelist$sample_class[samplelist$blank == "yes"])
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149
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150 chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class]
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151 if (length(chosen_blank) > 1) {
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152 print("ERROR: only 1 blank is currently allowed to be used with this tool")
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153 quit()
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154 }
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155 blank_class <- as.character(chosen_blank)
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156 print(blank_class)
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157 }
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158
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159
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160 if (is.null(opt$multilist)) {
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161 ffrm_out <- flag_remove(xset,
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162 pol = opt$polarity,
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163 rsd_i_blank = opt$rsd_i_blank,
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164 minfrac_blank = opt$minfrac_blank,
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165 rsd_rt_blank = opt$rsd_rt_blank,
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166 ithres_blank = opt$ithres_blank,
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167 s2b = opt$s2b,
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168 ref.class = blank_class,
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169 egauss_thr = opt$egauss_thr,
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170 rsd_i_sample = opt$rsd_i_sample,
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171 minfrac_sample = opt$minfrac_sample,
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172 rsd_rt_sample = opt$rsd_rt_sample,
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173 ithres_sample = opt$ithres_sample,
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174 minfrac_xcms = opt$minfrac_xcms,
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175 mzwid = opt$mzwid,
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176 bw = opt$bw,
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177 out_dir = opt$out_dir,
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178 temp_save = temp_save,
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179 remove_spectra = remove_spectra,
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180 grp_rm_ids = unlist(strsplit(as.character(opt$grp_rm_ids), split = ", "))[[1]]
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181 )
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182 print("flag remove finished")
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183 xset <- ffrm_out[[1]]
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184 grp_peaklist <- ffrm_out[[2]]
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185 removed_peaks <- ffrm_out[[3]]
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186
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187 save.image(file = file.path(opt$out_dir, "xset_filtered.RData"), version = 2)
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188
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189 # grpid needed for mspurity ID needed for deconrank... (will clean up at some up)
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190 peak_pth <- file.path(opt$out_dir, "peaklist_filtered.tsv")
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191 print(peak_pth)
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192 write.table(data.frame("grpid" = rownames(grp_peaklist), "ID" = rownames(grp_peaklist), grp_peaklist),
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193 peak_pth,
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194 row.names = FALSE, sep = "\t"
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195 )
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196
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197 removed_peaks <- data.frame(removed_peaks)
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198 write.table(data.frame("ID" = rownames(removed_peaks), removed_peaks),
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199 file.path(opt$out_dir, "removed_peaks.tsv"),
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200 row.names = FALSE, sep = "\t"
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201 )
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202 } else {
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203 # nolint start
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204 # TODO
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205 # xsets <- split(xset, multilist_df$multlist)
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206 #
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207 # mult_grps <- unique(multilist_df$multlist)
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208 #
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209 # for (mgrp in mult_grps){
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210 # xset_i <- xsets[mgrp]
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211 # xcms::group(xset_i,
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212 #
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213 # }
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214 # nolint end
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215 }