Mercurial > repos > computational-metabolomics > mspurity_flagremove

annotate combineAnnotations.R @ 9:da36e8bbcfbd draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author computational-metabolomics
date Thu, 13 Jun 2024 11:35:07 +0000
parents a0ee43397d1e
children
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
1 library(optparse)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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2 library(msPurity)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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3 print(sessionInfo())
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4
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5 # Get the parameter
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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6 option_list <- list(
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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7 make_option(c("-s", "--sm_resultPth"), type = "character"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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8 make_option(c("-m", "--metfrag_resultPth"), type = "character"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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9 make_option(c("-c", "--sirius_csi_resultPth"), type = "character"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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10 make_option(c("-p", "--probmetab_resultPth"), type = "character"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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11 make_option(c("-l", "--ms1_lookup_resultPth"), type = "character"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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12 make_option("--ms1_lookup_checkAdducts", action = "store_true"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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13 make_option("--ms1_lookup_keepAdducts", type = "character", default = NA),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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14 make_option("--ms1_lookup_dbSource", type = "character", default = "hmdb"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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15 make_option("--sm_weight", type = "numeric"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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16 make_option("--metfrag_weight", type = "numeric"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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17 make_option("--sirius_csi_weight", type = "numeric"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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18 make_option("--probmetab_weight", type = "numeric"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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19 make_option("--ms1_lookup_weight", type = "numeric"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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20 make_option("--biosim_weight", type = "numeric"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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21 make_option("--summaryOutput", action = "store_true"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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22 make_option("--create_new_database", action = "store_true"),
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23 make_option("--outdir", type = "character", default = "."),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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24 make_option("--compoundDbType", type = "character", default = "sqlite"),
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25 make_option("--compoundDbPth", type = "character", default = NA),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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26 make_option("--compoundDbHost", type = "character", default = NA)
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27 )
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28 opt <- parse_args(OptionParser(option_list = option_list))
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30 print(opt)
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32 if (!is.null(opt$create_new_database)) {
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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33 sm_resultPth <- file.path(opt$outdir, "combined_annotations.sqlite")
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34 file.copy(opt$sm_resultPth, sm_resultPth)
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35 } else {
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36 sm_resultPth <- opt$sm_resultPth
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37 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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38
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39 if (is.null(opt$ms1_lookup_checkAdducts)) {
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40 opt$ms1_lookup_checkAdducts <- FALSE
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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41 }
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42 if (!is.null(opt$ms1_lookup_keepAdducts)) {
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43 opt$ms1_lookup_keepAdducts <- gsub("__ob__", "[", opt$ms1_lookup_keepAdducts)
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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44 opt$ms1_lookup_keepAdducts <- gsub("__cb__", "]", opt$ms1_lookup_keepAdducts)
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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45 ms1_lookup_keepAdducts <- strsplit(opt$ms1_lookup_keepAdducts, ",")[[1]]
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46 }
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47
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48 weights <- list(
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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49 "sm" = opt$sm_weight,
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50 "metfrag" = opt$metfrag_weight,
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51 "sirius_csifingerid" = opt$sirius_csi_weight,
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52 "probmetab" = opt$probmetab_weight,
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53 "ms1_lookup" = opt$ms1_lookup_weight,
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54 "biosim" = opt$biosim_weight
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55 )
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56 print(weights)
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58 if (is.null(opt$probmetab_resultPth)) {
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59 opt$probmetab_resultPth <- NA
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60 }
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61
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62 if (round(!sum(unlist(weights), 0) == 1)) {
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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63 stop(paste0("The weights should sum to 1 not ", sum(unlist(weights))))
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64 }
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65
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66 if (is.null(opt$summaryOutput)) {
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67 summaryOutput <- FALSE
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68 } else {
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69 summaryOutput <- TRUE
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70 }
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71
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72 if (opt$compoundDbType == "local_config") {
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73 # load in compound config
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74 # Soure local function taken from workflow4metabolomics
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75 source_local <- function(fname) {
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76 argv <- commandArgs(trailingOnly = FALSE)
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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77 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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78 source(paste(base_dir, fname, sep = "/"))
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79 }
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80 source_local("dbconfig.R")
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81 } else {
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82 compoundDbPth <- opt$compoundDbPth
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83 compoundDbType <- opt$compoundDbType
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84 compoundDbName <- NA
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85 compoundDbHost <- NA
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86 compoundDbPort <- NA
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87 compoundDbUser <- NA
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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88 compoundDbPass <- NA
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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89 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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90
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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91 summary_output <- msPurity::combineAnnotations(
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a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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92 sm_resultPth = sm_resultPth,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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93 compoundDbPth = compoundDbPth,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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94 metfrag_resultPth = opt$metfrag_resultPth,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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95 sirius_csi_resultPth = opt$sirius_csi_resultPth,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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96 probmetab_resultPth = opt$probmetab_resultPth,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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97 ms1_lookup_resultPth = opt$ms1_lookup_resultPth,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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98 ms1_lookup_keepAdducts = ms1_lookup_keepAdducts,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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99 ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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100 compoundDbType = compoundDbType,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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101 compoundDbName = compoundDbName,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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102 compoundDbHost = compoundDbHost,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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103 compoundDbPort = compoundDbPort,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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104 compoundDbUser = compoundDbUser,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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105 compoundDbPass = compoundDbPass,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
106 weights = weights,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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107 summaryOutput = summaryOutput
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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108 )
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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109 if (summaryOutput) {
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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110 write.table(summary_output,
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a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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111 file.path(opt$outdir, "combined_annotations.tsv"),
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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112 sep = "\t", row.names = FALSE
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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113 )
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e570f604b357 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 242de155f13acd6cb88946e89b5196ac55578aa8"
computational-metabolomics
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114 }
e570f604b357 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 242de155f13acd6cb88946e89b5196ac55578aa8"
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115
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a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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116 write.table(summary_output,
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a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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117 file.path(opt$outdir, "combined_annotations.tsv"),
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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118 sep = "\t", row.names = FALSE
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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119 )
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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120
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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121 closeAllConnections()