Mercurial > repos > computational-metabolomics > mspurity_frag4feature
annotate flagRemove.R @ 0:ab65999a5430 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
author | computational-metabolomics |
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date | Wed, 27 Nov 2019 14:23:10 -0500 |
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children | 61ebae7e09f5 |
rev | line source |
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0
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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1 library(msPurity) |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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2 library(optparse) |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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3 print(sessionInfo()) |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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4 option_list <- list( |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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5 make_option(c("-o", "--out_dir"), type="character", default=getwd(), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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6 help="Output folder for resulting files [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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7 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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8 make_option(c("-x", "--xset_path"), type="character", default=file.path(getwd(),"xset.rds"), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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9 help="The path to the xcmsSet object [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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10 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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11 make_option("--polarity", default=NA, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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12 help="polarity (just used for naming purpose for files being saved) [positive, negative, NA] [default %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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13 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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14 make_option("--rsd_i_blank", default=100, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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15 help="RSD threshold for the blank [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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16 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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17 make_option("--minfrac_blank", default=0.5, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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18 help="minimum fraction of files for features needed for the blank [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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19 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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20 make_option("--rsd_rt_blank", default=100, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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21 help="RSD threshold for the RT of the blank [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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22 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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23 |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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24 make_option("--ithres_blank", default=0, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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25 help="Intensity threshold for the blank [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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26 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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27 make_option("--s2b", default=10, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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28 help="fold change (sample/blank) needed for sample peak to be allowed. e.g. |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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29 if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10. |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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30 1000/10 = 100, so sample has fold change higher than the threshold and the peak |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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31 is not considered a blank [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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32 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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33 make_option("--blank_class", default='blank', type="character", |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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34 help="A string representing the class that will be used for the blank.[default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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35 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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36 make_option("--egauss_thr", default=NA, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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37 help="Threshold for filtering out non gaussian shaped peaks. Note this only works |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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38 if the 'verbose columns' and 'fit gauss' was used with xcms |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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39 [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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40 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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41 make_option("--rsd_i_sample", default=100, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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42 help="RSD threshold for the samples [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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43 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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44 make_option("--minfrac_sample", default=0.8, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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45 help="minimum fraction of files for features needed for the samples [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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46 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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47 make_option("--rsd_rt_sample", default=100, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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48 help="RSD threshold for the RT of the samples [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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49 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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50 make_option("--ithres_sample", default=5000, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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51 help="Intensity threshold for the sample [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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52 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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53 make_option("--grp_rm_ids", default=NA, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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54 help="vector of grouped_xcms peaks to remove (corresponds to the row from xcms::group output) |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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55 [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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56 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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57 make_option("--remove_spectra", action="store_true", |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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58 help=" TRUE if flagged spectra is to be removed [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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59 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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60 make_option("--minfrac_xcms", default=0.5, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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61 help="minfrac for xcms grouping [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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62 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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63 make_option("--mzwid", default=0.001, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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64 help="mzwid for xcms grouping [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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65 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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66 make_option("--bw", default=5, |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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67 help="bw for xcms grouping [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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68 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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69 |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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70 make_option("--temp_save", action="store_true", |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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71 help="Assign True if files for each step saved (for testing purposes) [default = %default]" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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72 ), |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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73 |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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74 make_option("--samplelist", type="character", help="Sample list to determine the blank class") |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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75 |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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76 |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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77 |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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78 |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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79 |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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80 ) |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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81 |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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82 #make_option("--multilist", action="store_true" |
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83 # help="NOT CURRENTLY IMPLEMENTED: If paired blank removal is to be performed a - multilist - sample list file has to be provided" |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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84 #), |
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85 |
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86 # store options |
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87 opt<- parse_args(OptionParser(option_list=option_list)) |
ab65999a5430
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88 |
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89 opt <- replace(opt, opt == "NA", NA) |
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90 |
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91 |
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92 |
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93 |
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94 if (is.null(opt$temp_save)){ |
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95 temp_save<-FALSE |
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96 }else{ |
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97 temp_save<-TRUE |
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98 } |
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99 |
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100 if (is.null(opt$remove_spectra)){ |
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101 remove_spectra<-FALSE |
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102 }else{ |
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103 remove_spectra<-TRUE |
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104 } |
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105 |
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106 |
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107 print(opt) |
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108 |
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109 getxcmsSetObject <- function(xobject) { |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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110 # XCMS 1.x |
ab65999a5430
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111 if (class(xobject) == "xcmsSet") |
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112 return (xobject) |
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113 # XCMS 3.x |
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114 if (class(xobject) == "XCMSnExp") { |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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115 # Get the legacy xcmsSet object |
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116 suppressWarnings(xset <- as(xobject, 'xcmsSet')) |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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117 sampclass(xset) <- xset@phenoData$sample_group |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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118 return (xset) |
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119 } |
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120 } |
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121 |
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122 |
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123 loadRData <- function(rdata_path, name){ |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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124 #loads an RData file, and returns the named xset object if it is there |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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125 load(rdata_path) |
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126 return(get(ls()[ls() %in% name])) |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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127 } |
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128 |
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129 xset <- getxcmsSetObject(loadRData(opt$xset_path, c('xset','xdata'))) |
ab65999a5430
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130 |
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131 print(xset) |
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132 if (is.null(opt$samplelist)){ |
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133 blank_class <- opt$blank_class |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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134 }else{ |
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135 samplelist <- read.table(opt$samplelist, sep='\t', header=TRUE) |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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136 samplelist_blank <- unique(samplelist$sample_class[samplelist$blank=='yes']) |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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137 |
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138 chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class] |
ab65999a5430
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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139 if (length(chosen_blank)>1){ |
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140 print('ERROR: only 1 blank is currently allowed to be used with this tool') |
ab65999a5430
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141 exit() |
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142 } |
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143 blank_class <- as.character(chosen_blank) |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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144 print(blank_class) |
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145 } |
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146 |
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147 |
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148 if (is.null(opt$multilist)){ |
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149 ffrm_out <- flag_remove(xset, |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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150 pol=opt$polarity, |
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151 rsd_i_blank=opt$rsd_i_blank, |
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152 minfrac_blank=opt$minfrac_blank, |
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153 rsd_rt_blank=opt$rsd_rt_blank, |
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154 ithres_blank=opt$ithres_blank, |
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155 s2b=opt$s2b, |
ab65999a5430
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156 ref.class=blank_class, |
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157 egauss_thr=opt$egauss_thr, |
ab65999a5430
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158 rsd_i_sample=opt$rsd_i_sample, |
ab65999a5430
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159 minfrac_sample=opt$minfrac_sample, |
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160 rsd_rt_sample=opt$rsd_rt_sample, |
ab65999a5430
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161 ithres_sample=opt$ithres_sample, |
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162 minfrac_xcms=opt$minfrac_xcms, |
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163 mzwid=opt$mzwid, |
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164 bw=opt$bw, |
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165 out_dir=opt$out_dir, |
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166 temp_save=temp_save, |
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computational-metabolomics
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167 remove_spectra=remove_spectra, |
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168 grp_rm_ids=unlist(strsplit(as.character(opt$grp_rm_ids), split=", "))[[1]]) |
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169 print('flag remove finished') |
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170 xset <- ffrm_out[[1]] |
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171 grp_peaklist <- ffrm_out[[2]] |
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172 removed_peaks <- ffrm_out[[3]] |
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173 |
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174 save.image(file=file.path(opt$out_dir, 'xset_filtered.RData')) |
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175 |
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176 # grpid needed for mspurity ID needed for deconrank... (will clean up at some up) |
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177 peak_pth <- file.path(opt$out_dir, 'peaklist_filtered.tsv') |
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178 print(peak_pth) |
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179 write.table(data.frame('grpid'=rownames(grp_peaklist), 'ID'=rownames(grp_peaklist), grp_peaklist), |
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180 peak_pth, row.names=FALSE, sep='\t') |
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181 |
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182 removed_peaks <- data.frame(removed_peaks) |
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183 write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks), |
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184 file.path(opt$out_dir, 'removed_peaks.tsv'), row.names=FALSE, sep='\t') |
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185 |
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186 }else{ |
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187 |
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188 |
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189 # TODO |
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190 #xsets <- split(xset, multilist_df$multlist) |
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191 # |
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192 #mult_grps <- unique(multilist_df$multlist) |
ab65999a5430
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193 # |
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194 #for (mgrp in mult_grps){ |
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195 # xset_i <- xsets[mgrp] |
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196 # xcms::group(xset_i, |
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197 # |
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198 # } |
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199 |
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200 |
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201 |
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202 } |
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203 |
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204 |