Mercurial > repos > computational-metabolomics > mspurity_combineannotations

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:21:39 +0000
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de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
1 library(optparse)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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2 library(msPurity)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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3 print(sessionInfo())
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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4
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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5 # Get the parameter
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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6 option_list <- list(
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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7 make_option(c("-s", "--sm_resultPth"), type = "character"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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8 make_option(c("-m", "--metfrag_resultPth"), type = "character"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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9 make_option(c("-c", "--sirius_csi_resultPth"), type = "character"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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10 make_option(c("-p", "--probmetab_resultPth"), type = "character"),
de93f6aac760 "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"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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13 make_option("--ms1_lookup_checkAdducts", action = "store_true"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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14 make_option("--ms1_lookup_keepAdducts", type = "character", default = NA),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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15 make_option("--ms1_lookup_dbSource", type = "character", default = "hmdb"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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17 make_option("--sm_weight", type = "numeric"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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18 make_option("--metfrag_weight", type = "numeric"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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19 make_option("--sirius_csi_weight", type = "numeric"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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20 make_option("--probmetab_weight", type = "numeric"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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21 make_option("--ms1_lookup_weight", type = "numeric"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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22 make_option("--biosim_weight", type = "numeric"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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24 make_option("--summaryOutput", action = "store_true"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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26 make_option("--create_new_database", action = "store_true"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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27 make_option("--outdir", type = "character", default = "."),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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29 make_option("--compoundDbType", type = "character", default = "sqlite"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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30 make_option("--compoundDbPth", type = "character", default = NA),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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31 make_option("--compoundDbHost", type = "character", default = NA)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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32 )
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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33 opt <- parse_args(OptionParser(option_list = option_list))
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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35 print(opt)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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37 if (!is.null(opt$create_new_database)) {
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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38 sm_resultPth <- file.path(opt$outdir, "combined_annotations.sqlite")
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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39 file.copy(opt$sm_resultPth, sm_resultPth)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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40 }else{
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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41 sm_resultPth <- opt$sm_resultPth
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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42 }
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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43
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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44 if (is.null(opt$ms1_lookup_checkAdducts)) {
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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45 opt$ms1_lookup_checkAdducts <- FALSE
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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46 }
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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47 if (!is.null(opt$ms1_lookup_keepAdducts)) {
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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48 opt$ms1_lookup_keepAdducts <- gsub("__ob__", "[", opt$ms1_lookup_keepAdducts)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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49 opt$ms1_lookup_keepAdducts <- gsub("__cb__", "]", opt$ms1_lookup_keepAdducts)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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50 ms1_lookup_keepAdducts <- strsplit(opt$ms1_lookup_keepAdducts, ",")[[1]]
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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51 }
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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52
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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53 weights <- list("sm" = opt$sm_weight,
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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54 "metfrag" = opt$metfrag_weight,
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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55 "sirius_csifingerid" = opt$sirius_csi_weight,
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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56 "probmetab" = opt$probmetab_weight,
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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57 "ms1_lookup" = opt$ms1_lookup_weight,
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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58 "biosim" = opt$biosim_weight
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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59 )
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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60 print(weights)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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61
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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62 if (is.null(opt$probmetab_resultPth)) {
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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63 opt$probmetab_resultPth <- NA
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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64 }
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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65
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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66 if (round(!sum(unlist(weights), 0) == 1)) {
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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67 stop(paste0("The weights should sum to 1 not ", sum(unlist(weights))))
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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68 }
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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69
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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70 if (is.null(opt$summaryOutput)) {
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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71 summaryOutput <- FALSE
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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72 }else{
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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73 summaryOutput <- TRUE
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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74 }
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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75
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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76 if (opt$compoundDbType == "local_config") {
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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77 # load in compound config
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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78 # Soure local function taken from workflow4metabolomics
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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79 source_local <- function(fname) {
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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80 argv <- commandArgs(trailingOnly = FALSE)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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81 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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82 source(paste(base_dir, fname, sep = "/"))
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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83 }
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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84 source_local("dbconfig.R")
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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85 }else{
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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86 compoundDbPth <- opt$compoundDbPth
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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87 compoundDbType <- opt$compoundDbType
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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88 compoundDbName <- NA
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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89 compoundDbHost <- NA
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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90 compoundDbPort <- NA
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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91 compoundDbUser <- NA
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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92 compoundDbPass <- NA
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93 }
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94
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95 summary_output <- msPurity::combineAnnotations(
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96 sm_resultPth = sm_resultPth,
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97 compoundDbPth = compoundDbPth,
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98 metfrag_resultPth = opt$metfrag_resultPth,
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99 sirius_csi_resultPth = opt$sirius_csi_resultPth,
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100 probmetab_resultPth = opt$probmetab_resultPth,
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101 ms1_lookup_resultPth = opt$ms1_lookup_resultPth,
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102 ms1_lookup_keepAdducts = ms1_lookup_keepAdducts,
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103 ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts,
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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104
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105 compoundDbType = compoundDbType,
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106 compoundDbName = compoundDbName,
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107 compoundDbHost = compoundDbHost,
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108 compoundDbPort = compoundDbPort,
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109 compoundDbUser = compoundDbUser,
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110 compoundDbPass = compoundDbPass,
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111 weights = weights,
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112 summaryOutput = summaryOutput)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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113 if (summaryOutput) {
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114 write.table(summary_output,
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115 file.path(opt$outdir, "combined_annotations.tsv"),
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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116 sep = "\t", row.names = FALSE)
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117 }
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118
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119 write.table(summary_output,
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120 file.path(opt$outdir, "combined_annotations.tsv"),
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121 sep = "\t", row.names = FALSE)
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122
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123 closeAllConnections()