Mercurial > repos > computational-metabolomics > mspurity_filterfragspectra
annotate spectralMatching.R @ 8:a46824d13914 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
author | computational-metabolomics |
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date | Wed, 12 Jun 2024 16:09:13 +0000 |
parents | cc0f8ddad4a8 |
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rev | line source |
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0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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1 library(msPurity) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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2 library(msPurityData) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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3 library(optparse) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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4 print(sessionInfo()) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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5 # load in library spectra config |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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6 source_local <- function(fname) { |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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7 argv <- commandArgs(trailingOnly = FALSE) |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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8 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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9 source(paste(base_dir, fname, sep = "/")) |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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10 } |
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96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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11 source_local("dbconfig.R") |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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12 |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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13 option_list <- list( |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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14 make_option(c("-o", "--outDir"), type = "character"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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15 make_option("--q_dbPth", type = "character"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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16 make_option("--l_dbPth", type = "character"), |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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17 |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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18 make_option("--q_dbType", type = "character", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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19 make_option("--l_dbType", type = "character", default = NA), |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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20 |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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21 make_option("--q_msp", type = "character", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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22 make_option("--l_msp", type = "character", default = NA), |
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96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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23 |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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24 make_option("--q_defaultDb", action = "store_true"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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25 make_option("--l_defaultDb", action = "store_true"), |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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26 |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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27 make_option("--q_ppmPrec", type = "double"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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28 make_option("--l_ppmPrec", type = "double"), |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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30 make_option("--q_ppmProd", type = "double"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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31 make_option("--l_ppmProd", type = "double"), |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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32 |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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33 make_option("--q_raThres", type = "double", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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34 make_option("--l_raThres", type = "double", default = NA), |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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35 |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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36 make_option("--q_polarity", type = "character", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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37 make_option("--l_polarity", type = "character", default = NA), |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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38 |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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39 make_option("--q_purity", type = "double", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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40 make_option("--l_purity", type = "double", default = NA), |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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41 |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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42 make_option("--q_xcmsGroups", type = "character", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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43 make_option("--l_xcmsGroups", type = "character", default = NA), |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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44 |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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45 make_option("--q_pids", type = "character", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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46 make_option("--l_pids", type = "character", default = NA), |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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47 |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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48 make_option("--q_rtrangeMin", type = "double", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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49 make_option("--l_rtrangeMin", type = "double", default = NA), |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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50 |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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51 make_option("--q_rtrangeMax", type = "double", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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52 make_option("--l_rtrangeMax", type = "double", default = NA), |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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53 |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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54 make_option("--q_accessions", type = "character", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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55 make_option("--l_accessions", type = "character", default = NA), |
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96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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56 |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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57 make_option("--q_sources", type = "character", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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58 make_option("--l_sources", type = "character", default = NA), |
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96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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59 |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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60 make_option("--q_sourcesUser", type = "character", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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61 make_option("--l_sourcesUser", type = "character", default = NA), |
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96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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63 make_option("--q_instrumentTypes", type = "character", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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64 make_option("--l_instrumentTypes", type = "character", default = NA), |
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96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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66 make_option("--q_instrumentTypesUser", type = "character", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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67 make_option("--l_instrumentTypesUser", type = "character", default = NA), |
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96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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69 make_option("--q_instruments", type = "character", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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70 make_option("--l_instruments", type = "character", default = NA), |
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96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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71 |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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72 make_option("--q_spectraTypes", type = "character", default = NA), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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73 make_option("--l_spectraTypes", type = "character", default = NA), |
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96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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74 |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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75 make_option("--q_spectraFilter", action = "store_true"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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76 make_option("--l_spectraFilter", action = "store_true"), |
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96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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77 |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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78 make_option("--usePrecursors", action = "store_true"), |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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79 |
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80 make_option("--mzW", type = "double"), |
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81 make_option("--raW", type = "double"), |
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82 |
6
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83 make_option("--rttol", type = "double", default = NA), |
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84 |
6
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85 make_option("--updateDb", action = "store_true"), |
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86 make_option("--copyDb", action = "store_true"), |
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87 make_option("--cores", default = 1) |
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88 |
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89 |
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90 ) |
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91 |
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92 # store options |
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93 opt <- parse_args(OptionParser(option_list = option_list)) |
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94 |
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95 print(opt) |
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96 |
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97 # check if the sqlite databases have any spectra |
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98 checkSPeakMeta <- function(dbPth, nme) { |
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99 if (is.null(dbPth)) { |
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100 return(TRUE) |
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101 }else if ((file.exists(dbPth)) & (file.info(dbPth)$size > 0)) { |
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102 con <- DBI::dbConnect(RSQLite::SQLite(), dbPth) |
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103 if (DBI::dbExistsTable(con, "s_peak_meta")) { |
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104 spm <- DBI::dbGetQuery(con, "SELECT * FROM s_peak_meta ORDER BY ROWID ASC LIMIT 1") |
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105 return(TRUE) |
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106 }else if (DBI::dbExistsTable(con, "library_spectra_meta")) { |
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107 spm <- DBI::dbGetQuery(con, "SELECT * FROM library_spectra_meta ORDER BY ROWID ASC LIMIT 1") |
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108 return(TRUE) |
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109 }else{ |
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110 print(paste("No spectra available for ", nme)) |
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111 return(FALSE) |
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112 } |
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113 }else{ |
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114 print(paste("file empty or does not exist for", nme)) |
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115 return(FALSE) |
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116 } |
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117 |
6
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118 |
0
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119 } |
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120 |
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121 |
6
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122 addQueryNameColumn <- function(sm) { |
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123 if (is.null(sm$matchedResults) || length(sm$matchedResults) == 1 || nrow(sm$matchedResults) == 0) { |
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124 return(sm) |
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125 } |
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126 |
6
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127 con <- DBI::dbConnect(RSQLite::SQLite(), sm$q_dbPth) |
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128 if (DBI::dbExistsTable(con, "s_peak_meta")) { |
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129 spm <- DBI::dbGetQuery(con, "SELECT pid, name AS query_entry_name FROM s_peak_meta") |
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130 }else if (DBI::dbExistsTable(con, "library_spectra_meta")) { |
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131 spm <- DBI::dbGetQuery(con, "SELECT id AS pid, name AS query_entry_name FROM library_spectra_meta") |
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132 } |
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133 print(sm$matchedResults) |
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134 if ("pid" %in% colnames(sm$matchedResults)) { |
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135 sm$matchedResults <- merge(sm$matchedResults, spm, by.x = "pid", by.y = "pid") |
0
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136 }else{ |
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137 sm$matchedResults <- merge(sm$matchedResults, spm, by.x = "qpid", by.y = "pid") |
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138 } |
6
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139 |
0
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140 print(sm$xcmsMatchedResults) |
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141 if (is.null(sm$xcmsMatchedResults) || length(sm$xcmsMatchedResults) == 1 || nrow(sm$xcmsMatchedResults) == 0) { |
0
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142 return(sm) |
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143 }else{ |
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144 if ("pid" %in% colnames(sm$xcmsMatchedResults)) { |
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145 sm$xcmsMatchedResults <- merge(sm$xcmsMatchedResults, spm, by.x = "pid", by.y = "pid") |
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146 }else{ |
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147 sm$xcmsMatchedResults <- merge(sm$xcmsMatchedResults, spm, by.x = "qpid", by.y = "pid") |
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148 } |
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149 } |
6
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150 |
0
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151 return(sm) |
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152 |
0
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153 } |
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154 |
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155 |
6
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156 updateDbF <- function(q_con, l_con) { |
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157 message("Adding extra details to database") |
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158 q_con <- DBI::dbConnect(RSQLite::SQLite(), sm$q_dbPth) |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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159 if (DBI::dbExistsTable(q_con, "l_s_peak_meta")) { |
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160 l_s_peak_meta <- DBI::dbGetQuery(q_con, "SELECT * FROM l_s_peak_meta") |
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161 colnames(l_s_peak_meta)[1] <- "pid" |
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162 } |
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163 |
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164 l_con <- DBI::dbConnect(RSQLite::SQLite(), l_dbPth) |
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165 if (DBI::dbExistsTable(l_con, "s_peaks")) { |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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166 l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT * FROM s_peaks WHERE pid in (%s)", paste(unique(l_s_peak_meta$pid), collapse = ","))) |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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167 |
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168 }else if (DBI::dbExistsTable(l_con, "library_spectra")) { |
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169 l_s_peaks <- DBI::dbGetQuery(l_con, sprintf("SELECT * FROM library_spectra |
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170 WHERE library_spectra_meta_id in (%s)", paste(unique(l_s_peak_meta$pid), collapse = ","))) |
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171 }else{ |
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172 l_s_peaks <- NULL |
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173 } |
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174 |
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175 if (DBI::dbExistsTable(l_con, "source")) { |
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176 l_source <- DBI::dbGetQuery(l_con, "SELECT * FROM source") |
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177 }else if (DBI::dbExistsTable(l_con, "library_spectra_source")) { |
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178 l_source <- DBI::dbGetQuery(l_con, "SELECT * FROM library_spectra_source") |
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179 }else{ |
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180 l_source <- NULL |
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181 } |
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182 |
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183 if (!is.null(l_s_peaks)) { |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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184 DBI::dbWriteTable(q_con, name = "l_s_peaks", value = l_s_peaks, row.names = FALSE, append = TRUE) |
0
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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185 } |
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186 |
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187 if (!is.null(l_source)) { |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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188 DBI::dbWriteTable(q_con, name = "l_source", value = l_source, row.names = FALSE, append = TRUE) |
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189 } |
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190 |
0
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191 } |
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192 |
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193 |
6
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194 extractMultiple <- function(optParam) { |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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195 if (!is.na(optParam)) { |
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196 param <- trimws(strsplit(optParam, ",")[[1]]) |
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197 param <- param[param != ""] |
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198 }else { |
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199 param <- NA |
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200 } |
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201 return(param) |
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202 |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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203 } |
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204 |
6
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205 if (!is.null(opt$q_defaultDb)) { |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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206 q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package = "msPurityData") |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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207 q_dbType <- "sqlite" |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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208 }else if (!opt$q_dbType == "local_config") { |
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209 q_dbType <- opt$q_dbType |
96af79da0cc6
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210 q_dbPth <- opt$q_dbPth |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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211 } |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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212 |
6
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213 if (!is.null(opt$l_defaultDb)) { |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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214 l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package = "msPurityData") |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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215 l_dbType <- "sqlite" |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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216 }else if (!opt$l_dbType == "local_config") { |
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217 l_dbType <- opt$l_dbType |
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218 l_dbPth <- opt$l_dbPth |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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219 } |
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220 |
6
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221 q_spectraTypes <- extractMultiple(opt$q_spectraTypes) |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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222 l_spectraTypes <- extractMultiple(opt$l_spectraTypes) |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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223 |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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224 q_polarity <- extractMultiple(opt$q_polarity) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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225 l_polarity <- extractMultiple(opt$l_polarity) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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226 |
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227 q_xcmsGroups <- extractMultiple(opt$q_xcmsGroups) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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228 l_xcmsGroups <- extractMultiple(opt$l_xcmsGroups) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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229 |
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230 q_pids <- extractMultiple(opt$q_pids) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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231 l_pids <- extractMultiple(opt$l_pids) |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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232 |
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233 q_sources <- extractMultiple(opt$q_sources) |
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234 l_sources <- extractMultiple(opt$l_sources) |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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235 |
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236 q_sourcesUser <- extractMultiple(opt$q_sourcesUser) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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237 l_sourcesUser <- extractMultiple(opt$l_sourcesUser) |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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238 |
6
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239 q_sources <- c(q_sources, q_sourcesUser) |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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240 l_sources <- c(l_sources, l_sourcesUser) |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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241 |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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242 q_instrumentTypes <- extractMultiple(opt$q_instrumentTypes) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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243 l_instrumentTypes <- extractMultiple(opt$l_instrumentTypes) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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244 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
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245 q_instrumentTypes <- c(q_instrumentTypes, q_instrumentTypes) |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff
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246 l_instrumentTypes <- c(l_instrumentTypes, l_instrumentTypes) |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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247 |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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248 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff
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249 if (!is.null(opt$l_spectraFilter)) { |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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250 l_spectraFilter <- TRUE |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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251 }else{ |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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252 l_spectraFilter <- FALSE |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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253 } |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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254 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
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diff
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255 if (!is.null(opt$q_spectraFilter)) { |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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256 q_spectraFilter <- TRUE |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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257 }else{ |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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258 q_spectraFilter <- FALSE |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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259 } |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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260 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
changeset
|
261 if (!is.null(opt$updateDb)) { |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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262 updateDb <- TRUE |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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263 }else{ |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
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264 updateDb <- FALSE |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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265 } |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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266 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
changeset
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267 if (!is.null(opt$copyDb)) { |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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268 copyDb <- TRUE |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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269 }else{ |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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270 copyDb <- FALSE |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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|
271 } |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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272 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
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273 if (!is.null(opt$l_rtrangeMax)) { |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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274 l_rtrangeMax <- opt$l_rtrangeMax |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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275 }else{ |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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276 l_rtrangeMax <- NA |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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277 } |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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278 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
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279 if (!is.null(opt$q_rtrangeMax)) { |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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280 q_rtrangeMax <- opt$q_rtrangeMax |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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281 }else{ |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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282 q_rtrangeMax <- NA |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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283 } |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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284 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
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|
285 if (!is.null(opt$l_rtrangeMin)) { |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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286 l_rtrangeMin <- opt$l_rtrangeMin |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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|
287 }else{ |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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288 l_rtrangeMin <- NA |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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|
289 } |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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290 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
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291 if (!is.null(opt$q_rtrangeMin)) { |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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292 q_rtrangeMin <- opt$q_rtrangeMin |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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293 }else{ |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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294 q_rtrangeMin <- NA |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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|
295 } |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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296 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
changeset
|
297 q_check <- checkSPeakMeta(opt$q_dbPth, "query") |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
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|
298 l_check <- checkSPeakMeta(opt$l_dbPth, "library") |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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299 |
4
448363111457
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
computational-metabolomics
parents:
0
diff
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|
300 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
changeset
|
301 if (q_check && l_check) { |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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|
302 sm <- msPurity::spectralMatching( |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
303 q_purity = opt$q_purity, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
304 l_purity = opt$l_purity, |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
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|
305 |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
306 q_ppmProd = opt$q_ppmProd, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
307 l_ppmProd = opt$l_ppmProd, |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
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|
308 |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
309 q_ppmPrec = opt$q_ppmPrec, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
310 l_ppmPrec = opt$l_ppmPrec, |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
changeset
|
311 |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
312 q_raThres = opt$q_raThres, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
313 l_raThres = opt$l_raThres, |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
changeset
|
314 |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
315 q_pol = q_polarity, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
316 l_pol = l_polarity, |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
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|
317 |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
changeset
|
318 q_spectraFilter = q_spectraFilter, |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
changeset
|
319 l_spectraFilter = l_spectraFilter, |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
4
diff
changeset
|
320 |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
321 q_xcmsGroups = q_xcmsGroups, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
changeset
|
322 l_xcmsGroups = l_xcmsGroups, |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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323 |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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324 q_pids = q_pids, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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325 l_pids = l_pids, |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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326 |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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327 q_sources = q_sources, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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328 l_sources = l_sources, |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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329 |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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330 q_instrumentTypes = q_instrumentTypes, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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331 l_instrumentTypes = l_instrumentTypes, |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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332 |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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333 q_spectraTypes = q_spectraTypes, |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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334 l_spectraTypes = l_spectraTypes, |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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335 |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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336 l_rtrange = c(l_rtrangeMin, l_rtrangeMax), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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337 q_rtrange = c(q_rtrangeMin, q_rtrangeMax), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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338 |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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339 q_accessions = opt$q_accessions, |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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340 l_accessions = opt$l_accessions, |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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341 |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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342 raW = opt$raW, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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343 mzW = opt$mzW, |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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344 rttol = opt$rttol, |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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345 cores = opt$cores, |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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346 |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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347 copyDb = copyDb, |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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348 updateDb = updateDb, |
0
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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349 outPth = "db_with_spectral_matching.sqlite", |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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350 |
0
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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351 q_dbPth = q_dbPth, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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352 q_dbType = q_dbType, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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353 q_dbName = q_dbName, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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354 q_dbHost = q_dbHost, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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355 q_dbUser = q_dbUser, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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356 q_dbPass = q_dbPass, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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357 q_dbPort = q_dbPort, |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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358 |
0
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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359 l_dbPth = l_dbPth, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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360 l_dbType = l_dbType, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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361 l_dbName = l_dbName, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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362 l_dbHost = l_dbHost, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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363 l_dbUser = l_dbUser, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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364 l_dbPass = l_dbPass, |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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365 l_dbPort = l_dbPort |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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366 |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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367 ) |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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368 |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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369 sm <- addQueryNameColumn(sm) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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370 # Get name of the query results (and merged with the data frames) |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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371 write.table(sm$matchedResults, "matched_results.tsv", sep = "\t", row.names = FALSE, col.names = TRUE) |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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372 write.table(sm$xcmsMatchedResults, "xcms_matched_results.tsv", sep = "\t", row.names = FALSE, col.names = TRUE) |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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373 |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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374 if (updateDb) { |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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375 updateDbF(q_con, l_con) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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376 } |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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377 } |