Mercurial > repos > computational-metabolomics > mspurity_combineannotations
annotate spectralMatching.R @ 1:cf62d2c0104e draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
author | computational-metabolomics |
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date | Thu, 05 Dec 2019 07:47:31 -0500 |
parents | 7f3183988100 |
children | 20768ba7f0b4 |
rev | line source |
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0
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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1 library(msPurity) |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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2 library(msPurityData) |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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3 library(optparse) |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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4 print(sessionInfo()) |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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5 # load in library spectra config |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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6 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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7 source_local("dbconfig.R") |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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8 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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9 option_list <- list( |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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10 make_option(c("-o", "--outDir"), type="character"), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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11 make_option("--q_dbPth", type="character"), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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12 make_option("--l_dbPth", type="character"), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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13 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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14 make_option("--q_dbType", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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15 make_option("--l_dbType", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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16 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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17 make_option("--q_msp", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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18 make_option("--l_msp", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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19 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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20 make_option("--q_defaultDb", action="store_true"), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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21 make_option("--l_defaultDb", action="store_true"), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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22 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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23 make_option("--q_ppmPrec", type="double"), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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24 make_option("--l_ppmPrec", type="double"), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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25 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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26 make_option("--q_ppmProd", type="double"), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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27 make_option("--l_ppmProd", type="double"), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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28 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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29 make_option("--q_raThres", type="double", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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30 make_option("--l_raThres", type="double", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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31 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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32 make_option("--q_polarity", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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33 make_option("--l_polarity", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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34 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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35 make_option("--q_purity", type="double", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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36 make_option("--l_purity", type="double", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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37 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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38 make_option("--q_xcmsGroups", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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39 make_option("--l_xcmsGroups", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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40 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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41 make_option("--q_pids", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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42 make_option("--l_pids", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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43 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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44 make_option("--q_rtrangeMin", type="double", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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45 make_option("--l_rtrangeMin", type="double", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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46 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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47 make_option("--q_rtrangeMax", type="double", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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48 make_option("--l_rtrangeMax", type="double", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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49 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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50 make_option("--q_accessions", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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51 make_option("--l_accessions", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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52 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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53 make_option("--q_sources", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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54 make_option("--l_sources", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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55 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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56 make_option("--q_sourcesUser", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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57 make_option("--l_sourcesUser", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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58 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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59 make_option("--q_instrumentTypes", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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60 make_option("--l_instrumentTypes", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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61 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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62 make_option("--q_instrumentTypesUser", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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63 make_option("--l_instrumentTypesUser", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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64 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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65 make_option("--q_instruments", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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66 make_option("--l_instruments", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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67 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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68 make_option("--q_spectraTypes", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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69 make_option("--l_spectraTypes", type="character", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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70 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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71 make_option("--q_spectraFilter", action="store_true"), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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72 make_option("--l_spectraFilter", action="store_true"), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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73 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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74 make_option("--usePrecursors", action="store_true"), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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75 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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76 make_option("--mzW", type="double"), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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77 make_option("--raW", type="double"), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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78 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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79 make_option("--rttol", type="double", default=NA), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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80 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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81 make_option("--updateDb", action="store_true"), |
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82 make_option("--copyDb", action="store_true"), |
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83 make_option("--cores", default=1) |
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84 |
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85 |
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86 ) |
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87 |
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88 # store options |
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89 opt<- parse_args(OptionParser(option_list=option_list)) |
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90 |
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91 print(opt) |
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92 |
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93 # check if the sqlite databases have any spectra |
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94 checkSPeakMeta <- function(dbPth, nme){ |
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95 if(is.null(dbPth)){ |
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96 return(TRUE) |
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97 }else if ((file.exists(dbPth)) & (file.info(dbPth)$size>0)){ |
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98 con <- DBI::dbConnect(RSQLite::SQLite(), dbPth) |
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99 if (DBI::dbExistsTable(con, "s_peak_meta")){ |
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100 spm <- DBI::dbGetQuery(con, 'SELECT * FROM s_peak_meta ORDER BY ROWID ASC LIMIT 1') |
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101 return(TRUE) |
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102 }else if(DBI::dbExistsTable(con, "library_spectra_meta")){ |
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103 spm <- DBI::dbGetQuery(con, 'SELECT * FROM library_spectra_meta ORDER BY ROWID ASC LIMIT 1') |
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104 return(TRUE) |
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105 }else{ |
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106 print(paste("No spectra available for ",nme)) |
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107 return(FALSE) |
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108 } |
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109 }else{ |
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110 print(paste("file empty or does not exist for", nme)) |
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111 return(FALSE) |
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112 } |
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113 |
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114 |
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115 } |
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116 |
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117 |
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118 addQueryNameColumn <- function(sm){ |
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119 if (is.null(sm$matchedResults) || length(sm$matchedResults)==1 || nrow(sm$matchedResults)==0){ |
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120 return(sm) |
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121 } |
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122 |
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123 con <- DBI::dbConnect(RSQLite::SQLite(),sm$q_dbPth) |
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124 if (DBI::dbExistsTable(con, "s_peak_meta")){ |
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125 spm <- DBI::dbGetQuery(con, 'SELECT pid, name AS query_entry_name FROM s_peak_meta') |
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126 }else if(DBI::dbExistsTable(con, "library_spectra_meta")){ |
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127 spm <- DBI::dbGetQuery(con, 'SELECT id AS pid, name AS query_entry_name FROM library_spectra_meta') |
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128 } |
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129 print(sm$matchedResults) |
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130 if ('pid' %in% colnames(sm$matchedResults)){ |
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131 sm$matchedResults <- merge(sm$matchedResults, spm, by.x='pid', by.y='pid') |
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132 }else{ |
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133 sm$matchedResults <- merge(sm$matchedResults, spm, by.x='qpid', by.y='pid') |
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134 } |
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135 |
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136 print(sm$xcmsMatchedResults) |
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137 if (is.null(sm$xcmsMatchedResults) || length(sm$xcmsMatchedResults)==1 || nrow(sm$xcmsMatchedResults)==0){ |
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138 return(sm) |
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139 }else{ |
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140 if ('pid' %in% colnames(sm$xcmsMatchedResults)){ |
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141 sm$xcmsMatchedResults<- merge(sm$xcmsMatchedResults, spm, by.x='pid', by.y='pid') |
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142 }else{ |
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143 sm$xcmsMatchedResults <- merge(sm$xcmsMatchedResults, spm, by.x='qpid', by.y='pid') |
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144 } |
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145 } |
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146 |
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147 return(sm) |
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148 |
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149 } |
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150 |
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151 |
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152 updateDbF <- function(q_con, l_con){ |
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153 message('Adding extra details to database') |
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154 q_con <- DBI::dbConnect(RSQLite::SQLite(),sm$q_dbPth) |
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155 if (DBI::dbExistsTable(q_con, "l_s_peak_meta")){ |
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156 l_s_peak_meta <- DBI::dbGetQuery(q_con, 'SELECT * FROM l_s_peak_meta') |
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157 colnames(l_s_peak_meta)[1] <- 'pid' |
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158 } |
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159 |
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160 l_con <- DBI::dbConnect(RSQLite::SQLite(),l_dbPth) |
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161 if (DBI::dbExistsTable(l_con, "s_peaks")){ |
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162 l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT * FROM s_peaks WHERE pid in (%s)", paste(unique(l_s_peak_meta$pid), collapse=','))) |
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163 |
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164 }else if(DBI::dbExistsTable(l_con, "library_spectra")){ |
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165 l_s_peaks <- DBI::dbGetQuery(l_con, sprintf("SELECT * FROM library_spectra |
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166 WHERE library_spectra_meta_id in (%s)", paste(unique(l_s_peak_meta$pid), collapse=','))) |
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167 }else{ |
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168 l_s_peaks = NULL |
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169 } |
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170 |
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171 if (DBI::dbExistsTable(l_con, "source")){ |
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172 l_source <- DBI::dbGetQuery(l_con, 'SELECT * FROM source') |
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173 }else if (DBI::dbExistsTable(l_con, "library_spectra_source")) { |
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174 l_source <- DBI::dbGetQuery(l_con, 'SELECT * FROM library_spectra_source') |
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175 }else{ |
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176 l_source = NULL |
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177 } |
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178 |
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179 if (!is.null(l_s_peaks)){ |
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180 DBI::dbWriteTable(q_con, name='l_s_peaks', value=l_s_peaks, row.names=FALSE, append=TRUE) |
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181 } |
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182 |
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183 if (!is.null(l_source)){ |
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184 DBI::dbWriteTable(q_con, name='l_source', value=l_source, row.names=FALSE, append=TRUE) |
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185 } |
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186 |
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187 |
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188 } |
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189 |
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190 |
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191 extractMultiple <- function(optParam){ |
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192 if (!is.na(optParam)){ |
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193 param <- trimws(strsplit(optParam, ',')[[1]]) |
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194 param <- param[param != ""] |
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195 }else{ |
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196 param <- NA |
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197 } |
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198 return(param) |
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199 |
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200 } |
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201 |
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202 if(!is.null(opt$q_defaultDb)){ |
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203 q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData") |
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204 q_dbType <- 'sqlite' |
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205 }else if (!opt$q_dbType=='local_config'){ |
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206 q_dbType <- opt$q_dbType |
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207 q_dbPth <- opt$q_dbPth |
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208 } |
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209 |
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210 if(!is.null(opt$l_defaultDb)){ |
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211 l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData") |
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212 l_dbType <- 'sqlite' |
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213 }else if (!opt$l_dbType=='local_config'){ |
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214 l_dbType <- opt$l_dbType |
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215 l_dbPth <- opt$l_dbPth |
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216 } |
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217 |
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218 |
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219 q_polarity <- extractMultiple(opt$q_polarity) |
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220 l_polarity <- extractMultiple(opt$l_polarity) |
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221 |
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222 q_xcmsGroups <- extractMultiple(opt$q_xcmsGroups) |
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223 l_xcmsGroups <- extractMultiple(opt$l_xcmsGroups) |
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224 |
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225 q_pids <- extractMultiple(opt$q_pids) |
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226 l_pids <- extractMultiple(opt$l_pids) |
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227 |
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228 q_sources <- extractMultiple(opt$q_sources) |
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229 l_sources <- extractMultiple(opt$l_sources) |
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230 |
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231 q_sourcesUser <- extractMultiple(opt$q_sourcesUser) |
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232 l_sourcesUser <- extractMultiple(opt$l_sourcesUser) |
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233 |
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234 q_sources <-c(q_sources, q_sourcesUser) |
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235 l_sources <-c(l_sources, l_sourcesUser) |
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236 |
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237 q_instrumentTypes <- extractMultiple(opt$q_instrumentTypes) |
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238 l_instrumentTypes <- extractMultiple(opt$l_instrumentTypes) |
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239 |
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240 q_instrumentTypes <-c(q_instrumentTypes, q_instrumentTypes) |
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241 l_instrumentTypes <-c(l_instrumentTypes, l_instrumentTypes) |
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242 |
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243 |
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244 if(!is.null(opt$l_spectraFilter)){ |
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245 l_spectraFilter <- TRUE |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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246 }else{ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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247 l_spectraFilter <- FALSE |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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248 } |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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249 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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250 if(!is.null(opt$q_spectraFilter)){ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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251 q_spectraFilter <- TRUE |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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252 }else{ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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253 q_spectraFilter <- FALSE |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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254 } |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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255 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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256 if(!is.null(opt$updateDb)){ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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257 updateDb <- TRUE |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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258 }else{ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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259 updateDb <- FALSE |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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260 } |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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261 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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262 if(!is.null(opt$copyDb)){ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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263 copyDb <- TRUE |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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264 }else{ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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265 copyDb <- FALSE |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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266 } |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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267 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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268 if(!is.null(opt$l_rtrangeMax)){ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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269 l_rtrangeMax <- opt$l_rtrangeMax |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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270 }else{ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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271 l_rtrangeMax <- NA |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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272 } |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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273 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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274 if(!is.null(opt$q_rtrangeMax)){ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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275 q_rtrangeMax <- opt$q_rtrangeMax |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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276 }else{ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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277 q_rtrangeMax <- NA |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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278 } |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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279 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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280 if(!is.null(opt$l_rtrangeMin)){ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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281 l_rtrangeMin <- opt$l_rtrangeMin |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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282 }else{ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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283 l_rtrangeMin <- NA |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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284 } |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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285 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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286 if(!is.null(opt$q_rtrangeMin)){ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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287 q_rtrangeMin <- opt$q_rtrangeMin |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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288 }else{ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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289 q_rtrangeMin <- NA |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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290 } |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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291 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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292 q_check <- checkSPeakMeta(opt$q_dbPth, 'query') |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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293 l_check <- checkSPeakMeta(opt$l_dbPth, 'library') |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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294 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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295 if (q_check && l_check){ |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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296 sm <- msPurity::spectralMatching( |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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297 q_purity = opt$q_purity, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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298 l_purity = opt$l_purity, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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299 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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300 q_ppmProd = opt$q_ppmProd, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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301 l_ppmProd = opt$l_ppmProd, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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302 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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303 q_ppmPrec = opt$q_ppmPrec, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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304 l_ppmPrec = opt$l_ppmPrec, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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305 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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306 q_raThres = opt$q_raThres, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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307 l_raThres = opt$l_raThres, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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|
308 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
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309 q_pol = q_polarity, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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310 l_pol = l_polarity, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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311 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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312 q_xcmsGroups = q_xcmsGroups, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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313 l_xcmsGroups = l_xcmsGroups, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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314 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
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315 q_pids = q_pids, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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316 l_pids = l_pids, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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317 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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318 q_sources = q_sources, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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319 l_sources = l_sources, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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320 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
321 q_instrumentTypes = q_instrumentTypes, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
322 l_instrumentTypes = l_instrumentTypes, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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|
323 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
324 q_spectraFilter= q_spectraFilter, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
325 l_spectraFilter= l_spectraFilter, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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|
326 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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327 l_rtrange=c(l_rtrangeMin, l_rtrangeMax), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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|
328 q_rtrange=c(q_rtrangeMin, q_rtrangeMax), |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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|
329 |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
330 q_accessions = opt$q_accessions, |
7f3183988100
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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331 l_accessions= opt$l_accessions, |
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332 |
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333 raW = opt$raW, |
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334 mzW = opt$mzW, |
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335 rttol=opt$rttol, |
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336 cores=opt$cores, |
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337 |
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338 copyDb=copyDb, |
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339 updateDb=updateDb, |
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340 outPth = "db_with_spectral_matching.sqlite", |
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341 |
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342 q_dbPth = q_dbPth, |
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343 q_dbType = q_dbType, |
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344 q_dbName = q_dbName, |
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345 q_dbHost = q_dbHost, |
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346 q_dbUser = q_dbUser, |
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347 q_dbPass = q_dbPass, |
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348 q_dbPort = q_dbPort, |
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349 |
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350 l_dbPth = l_dbPth, |
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351 l_dbType = l_dbType, |
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352 l_dbName = l_dbName, |
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353 l_dbHost = l_dbHost, |
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354 l_dbUser = l_dbUser, |
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355 l_dbPass = l_dbPass, |
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356 l_dbPort = l_dbPort |
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357 |
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358 ) |
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359 |
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360 sm <- addQueryNameColumn(sm) |
7f3183988100
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361 # Get name of the query results (and merged with the data frames) |
7f3183988100
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362 write.table(sm$matchedResults, 'matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE) |
7f3183988100
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363 write.table(sm$xcmsMatchedResults, 'xcms_matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE) |
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364 |
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365 if(updateDb){ |
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366 updateDbF(q_con, l_con) |
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367 } |
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368 } |