Mercurial > repos > marie-tremblay-metatoul > 2dnmrannotation

annotate annotationRmn2DWrapper.R @ 3:546c7ccd2ed4 draft default tip

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"planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
author workflow4metabolomics
date Fri, 04 Feb 2022 09:01:11 +0000
parents dff7bde22102
children
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dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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1 #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
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dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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3 ## 201919016 2DNmrAnnotation_1.0.0.R
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4 ## Marie Tremblay-Franco
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5 ## MetaboHUB: The French Infrastructure for Metabolomics and Fluxomics
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6 ## marie.tremblay-franco@inrae.fr
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dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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8 runExampleL <- FALSE
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10 if (runExampleL) {
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11 ##------------------------------
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12 ## Example of arguments
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13 ##------------------------------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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14 }
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dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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17 ##------------------------------
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18 ## Options
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19 ##------------------------------
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20 strAsFacL <- options()$stringsAsFactors
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21 options(stringsAsFactors = FALSE)
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22 options(digits = 8, scipen = 3)
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24 ##------------------------------
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25 ## Constants
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26 ##------------------------------
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27 topEnvC <- environment()
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28 flagC <- "\n"
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31 ##-------------------------
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32 ## Input parameters reading
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33 ##-------------------------
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dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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35 ##------------------------------
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36 ## R libraries laoding
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37 ##------------------------------
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38 library(batch)
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39 library(dplyr)
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40 library(ggplot2)
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41 library(openxlsx)
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42 library(stringr)
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43 library(tidyr)
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44 library(curl)
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45 library(jsonlite)
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46 library(stringi)
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47
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48 if (!runExampleL)
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49 argLs <- parseCommandArgs(evaluate = FALSE)
2
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50 logFile <- argLs[["logOut"]]
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51 sink(logFile)
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52
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53 cat("\tPACKAGE INFO\n")
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54 sessionInfo()
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55
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56 ##------------------------------
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57 ## Functions
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58 ##------------------------------
3
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59 source_local <- function(fname) {
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60 argv <- commandArgs(trailingOnly = FALSE)
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61 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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62 source(paste(base_dir, fname, sep = "/"))
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63 }
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64 #Import the different functions
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65 source_local("annotationRmn2D.R")
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66 source_local("annotationRmn2DGlobale.R")
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67 source_local("viridis.R")
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68
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69 ## Input parameter values
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70 fileToAnnotate <- argLs[[1]]
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71 # Constraints values
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72 ph <- argLs$pH
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73 field <- argLs$magneticField
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74
2
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75 # Chosen sequence(s)
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76 cosy <- 0
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77 hmbc <- 0
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78 hsqc <- 0
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79 jres <- 0
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80 tocsy <- 0
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81
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82 if (argLs$cosy_2dsequences == "yes") {
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83 cosy <- 1
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84 peakforestSpectra <- readLines(curl("https://metabohub.peakforest.org/rest/v1/spectra/nmr2d/search?query=cosy&token=9131jq9l8gsjn1j14t351h716u&max=500"))
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85 peakforestSpectra <- fromJSON(peakforestSpectra, simplifyDataFrame = TRUE)
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86 if (ph != 0)
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87 peakforestSpectra <- peakforestSpectra[peakforestSpectra$sampleNMRTubeConditionsMetadata$potentiaHydrogenii == ph, ]
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88 if (field != 0)
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89 peakforestSpectra <- peakforestSpectra[peakforestSpectra$analyzerNMRSpectrometerDevice$magneticFieldStrenght == field, ]
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90
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91 if (nrow(peakforestSpectra) != 0) {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
92 BdDReference_COSY <- peakforestSpectra$peaks
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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93 names(BdDReference_COSY) <- str_split(peakforestSpectra[, 2], simplify = TRUE, pattern = ";")[, 1]
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
94 names(BdDReference_COSY) <- enc2utf8(names(BdDReference_COSY))
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
parents: 2
diff changeset
95 names(BdDReference_COSY) <- str_replace_all(names(BdDReference_COSY), "\u00e9", "e")
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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96
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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97 for (k in seq_len(length(BdDReference_COSY))) {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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98 peakforestSpectra_df <- data.frame(ppm.dim1 = BdDReference_COSY[[k]][, 2], ppm.dim2 = BdDReference_COSY[[k]][, 1],
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
99 BdDReference_COSY[[k]][, 3:ncol(BdDReference_COSY[[k]])])
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
100 BdDReference_COSY[[k]] <- peakforestSpectra_df
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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101 }
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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102 } else {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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103 stop("No COSY spectra correspond to requested pH and/or magnetic field", call. = FALSE)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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104 }
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
105 rm(peakforestSpectra)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
106 rm(peakforestSpectra_df)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
107 }
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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108
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
109 if (argLs$hmbc_2dsequences == "yes") {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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110 hmbc <- 1
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
111 peakforestSpectra <- readLines(curl("https://metabohub.peakforest.org/rest/v1/spectra/nmr2d/search?query=hmbc&token=9131jq9l8gsjn1j14t351h716u&max=500"))
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
112 peakforestSpectra <- fromJSON(peakforestSpectra, simplifyDataFrame = TRUE)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
113 if (ph != 0)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
parents: 2
diff changeset
114 peakforestSpectra <- peakforestSpectra[peakforestSpectra$sampleNMRTubeConditionsMetadata$potentiaHydrogenii == ph, ]
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
115 if (field != 0)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
116 peakforestSpectra <- peakforestSpectra[peakforestSpectra$analyzerNMRSpectrometerDevice$magneticFieldStrenght == field, ]
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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117
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
118 if (nrow(peakforestSpectra) != 0) {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
119
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
120 BdDReference_HMBC <- peakforestSpectra$peaks
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
121 names(BdDReference_HMBC) <- str_split(peakforestSpectra[, 2], simplify = TRUE, pattern = ";")[, 1]
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
122 names(BdDReference_HMBC) <- enc2utf8(names(BdDReference_HMBC))
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
parents: 2
diff changeset
123 names(BdDReference_HMBC) <- str_replace_all(names(BdDReference_HMBC), "\u00e9", "e")
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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124
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
125 peakforestSpectra_df <- data.frame()
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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diff changeset
126 for (k in seq_len(length(BdDReference_HMBC))) {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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127 peakforestSpectra_df <- data.frame(ppm.dim1 = BdDReference_HMBC[[k]][, 2], ppm.dim2 = BdDReference_HMBC[[k]][, 1],
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
128 BdDReference_HMBC[[k]][, 3:ncol(BdDReference_HMBC[[k]])])
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
129 BdDReference_HMBC[[k]] <- peakforestSpectra_df
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
130 }
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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131 } else {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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132 stop("No HMBC spectra correspond to requested pH and/or magnetic field", call. = FALSE)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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133 }
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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diff changeset
134 rm(peakforestSpectra)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
135 rm(peakforestSpectra_df)
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
136 }
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
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137
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
138 if (argLs$hsqc_2dsequences == "yes") {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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139 hsqc <- 1
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
140 peakforestSpectra <- readLines(curl("https://metabohub.peakforest.org/rest/v1/spectra/nmr2d/search?query=hsqc&token=9131jq9l8gsjn1j14t351h716u&max=500"))
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
141 peakforestSpectra <- fromJSON(peakforestSpectra, simplifyDataFrame = TRUE)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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142
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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diff changeset
143 if (ph != 0)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
144 peakforestSpectra <- peakforestSpectra[peakforestSpectra$sampleNMRTubeConditionsMetadata$potentiaHydrogenii == ph, ]
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
145 if (field != 0)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
146 peakforestSpectra <- peakforestSpectra[peakforestSpectra$analyzerNMRSpectrometerDevice$magneticFieldStrenght == field, ]
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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147
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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diff changeset
148 if (nrow(peakforestSpectra) != 0) {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
149 BdDReference_HSQC <- peakforestSpectra$peaks
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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diff changeset
150 names(BdDReference_HSQC) <- str_split(peakforestSpectra[, 2], simplify = TRUE, pattern = ";")[, 1]
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
151 names(BdDReference_HSQC) <- enc2utf8(names(BdDReference_HSQC))
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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152 names(BdDReference_HSQC) <- str_replace_all(names(BdDReference_HSQC), "\u00e9", "e")
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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153
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
154 for (k in seq_len(length(BdDReference_HSQC))) {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
155 peakforestSpectra_df <- data.frame(ppm.dim1 = BdDReference_HSQC[[k]][, 2], ppm.dim2 = BdDReference_HSQC[[k]][, 1],
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
156 BdDReference_HSQC[[k]][, 3:ncol(BdDReference_HSQC[[k]])])
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
157 BdDReference_HSQC[[k]] <- peakforestSpectra_df
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
158 }
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
159 } else {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
160 stop("No HSQC spectra correspond to requested pH and/or magnetic field", call. = FALSE)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
parents: 2
diff changeset
161 }
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
162 rm(peakforestSpectra)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
163 rm(peakforestSpectra_df)
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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diff changeset
164 }
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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165
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
166 if (argLs$jres_2dsequences == "yes") {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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diff changeset
167 jres <- 1
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
168 peakforestSpectra <- readLines(curl("https://metabohub.peakforest.org/rest/v1/spectra/nmr2d/search?query=jres&token=9131jq9l8gsjn1j14t351h716u&max=500"))
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
169 peakforestSpectra <- fromJSON(peakforestSpectra, simplifyDataFrame = TRUE)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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170
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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diff changeset
171 if (ph != 0)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
172 peakforestSpectra <- peakforestSpectra[peakforestSpectra$sampleNMRTubeConditionsMetadata$potentiaHydrogenii == ph, ]
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
173 if (field != 0)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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diff changeset
174 peakforestSpectra <- peakforestSpectra[peakforestSpectra$analyzerNMRSpectrometerDevice$magneticFieldStrenght == field, ]
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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175
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176 if (nrow(peakforestSpectra) != 0) {
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177 BdDReference_JRES <- peakforestSpectra$peaks
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178 names(BdDReference_JRES) <- str_split(peakforestSpectra[, 2], simplify = TRUE, pattern = ";")[, 1]
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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179 names(BdDReference_JRES) <- enc2utf8(names(BdDReference_JRES))
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180 names(BdDReference_JRES) <- str_replace_all(names(BdDReference_JRES), "\u00e9", "e")
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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181
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182 for (k in seq_len(length(BdDReference_JRES))) {
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183 peakforestSpectra_df <- data.frame(ppm.dim1 = BdDReference_JRES[[k]][, 2], ppm.dim2 = BdDReference_JRES[[k]][, 1],
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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184 BdDReference_JRES[[k]][, 3:ncol(BdDReference_JRES[[k]])])
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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185 BdDReference_JRES[[k]] <- peakforestSpectra_df
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186 }
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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187 } else {
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188 stop("No JRES spectra correspond to requested pH and/or magnetic field", call. = FALSE)
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189 }
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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190 rm(peakforestSpectra)
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191 rm(peakforestSpectra_df)
2
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192 }
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193
3
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194 if (argLs$tocsy_2dsequences == "yes") {
2
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195 tocsy <- 1
3
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196 peakforestSpectra <- readLines(curl("https://metabohub.peakforest.org/rest/v1/spectra/nmr2d/search?query=tocsy&token=9131jq9l8gsjn1j14t351h716u&max=500"))
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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197 peakforestSpectra <- fromJSON(peakforestSpectra, simplifyDataFrame = TRUE)
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198
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199 if (ph != 0)
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200 peakforestSpectra <- peakforestSpectra[peakforestSpectra$sampleNMRTubeConditionsMetadata$potentiaHydrogenii == ph, ]
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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201 if (field != 0)
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202 peakforestSpectra <- peakforestSpectra[peakforestSpectra$analyzerNMRSpectrometerDevice$magneticFieldStrenght == field, ]
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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203
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204 if (nrow(peakforestSpectra) != 0) {
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205 BdDReference_TOCSY <- peakforestSpectra$peaks
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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206 names(BdDReference_TOCSY) <- str_split(peakforestSpectra[, 2], simplify = TRUE, pattern = ";")[, 1]
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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207 names(BdDReference_TOCSY) <- enc2utf8(names(BdDReference_TOCSY))
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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208 names(BdDReference_TOCSY) <- str_replace_all(names(BdDReference_TOCSY), "\u00e9", "e")
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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209
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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210 for (k in seq_len(length(BdDReference_TOCSY))) {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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211 peakforestSpectra_df <- data.frame(ppm.dim1 = BdDReference_TOCSY[[k]][, 2], ppm.dim2 = BdDReference_TOCSY[[k]][, 1],
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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212 BdDReference_TOCSY[[k]][, 3:ncol(BdDReference_TOCSY[[k]])])
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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213 BdDReference_TOCSY[[k]] <- peakforestSpectra_df
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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214 }
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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215 } else {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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216 stop("No TOCSY spectra correspond to requested pH and/or magnetic field", call. = FALSE)
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217 }
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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218 rm(peakforestSpectra)
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219 rm(peakforestSpectra_df)
2
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220 }
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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221
3
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222 if (argLs$cosy_2dsequences == "no" & argLs$hmbc_2dsequences == "no" & argLs$hsqc_2dsequences == "no" & argLs$jres_2dsequences == "no" & argLs$tocsy_2dsequences == "no")
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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223 stop("No chosen sequence. You have to choose at least 1 sequence", call. = FALSE)
2
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224
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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225
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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226 # User database
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227
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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228
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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229 # Allowed chemical shifts
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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230 tolPpm1 <- argLs$tolppm1
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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231 tolPpm2HJRes <- argLs$tolppmJRES
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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232 tolPpm2C <- argLs$tolppm2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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233 # Threshold to remove metabolites (probability score < threshold)
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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234 seuil <- argLs$threshold
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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235 # Remove metabolites when multiple assignations?
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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236 unicite <- str_to_upper(argLs$unicity)
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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237
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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238 ## Output paramater values
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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239 AnnotationGraph <- argLs[["AnnotationGraph"]]
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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240
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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241 print(argLs)
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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242
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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243 ## ANNOTATION
3
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244 st0 <- Sys.time()
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245 pdf(AnnotationGraph, onefile = TRUE)
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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246 annotationMelange <- annotationRmn2DGlobale(fileToAnnotate, tolPpm1 = tolPpm1, tolPpm2HJRes = tolPpm2HJRes,
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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247 tolPpm2C = tolPpm2C, cosy = cosy, hmbc = hmbc, hsqc = hsqc,
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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248 jres = jres, tocsy = tocsy, seuil = seuil, unicite = unicite)
2
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249 dev.off()
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250
3
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251 if (cosy == 1) {
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252 write.table(annotationMelange$COSY$liste_resultat, file = argLs[["annotationCOSY"]], quote = FALSE,
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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253 row.names = FALSE, sep = "\t")
2
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254 if (nrow(annotationMelange$COSY$listing_ppm_commun) != 0)
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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255 write.table(annotationMelange$COSY$listing_ppm_commun, file = argLs[["ppmCommunCOSY"]], quote = FALSE,
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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256 row.names = FALSE, sep = "\t")
2
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257 }
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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258
3
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259 if (hmbc == 1) {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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260 write.table(annotationMelange$HMBC$liste_resultat, file = argLs[["annotationHMBC"]], quote = FALSE,
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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261 row.names = FALSE, sep = "\t")
2
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262 if (nrow(annotationMelange$HMBC$listing_ppm_commun) != 0)
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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263 write.table(annotationMelange$HMBC$listing_ppm_commun, file = argLs[["ppmCommunHMBC"]], quote = FALSE,
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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264 row.names = FALSE, sep = "\t")
2
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265 }
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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266
3
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267 if (hsqc == 1) {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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268 write.table(annotationMelange$HSQC$liste_resultat, file = argLs[["annotationHSQC"]], quote = FALSE,
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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269 row.names = FALSE, sep = "\t")
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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270 if (nrow(annotationMelange$HSQC$listing_ppm_commun) != 0)
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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271 write.table(annotationMelange$HSQC$listing_ppm_commun, file = argLs[["ppmCommunHSQC"]], quote = FALSE,
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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272 row.names = FALSE, sep = "\t")
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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273 }
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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274
3
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275 if (jres == 1) {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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276 write.table(annotationMelange$JRES$liste_resultat, file = argLs[["annotationJRES"]], quote = FALSE,
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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277 row.names = FALSE, sep = "\t")
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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278 if (nrow(annotationMelange$JRES$listing_ppm_commun) != 0)
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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279 write.table(annotationMelange$JRES$listing_ppm_commun, file = argLs[["ppmCommunJRES"]], quote = FALSE,
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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280 row.names = FALSE, sep = "\t")
2
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281 }
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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282
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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283 if (tocsy == 1) {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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284 write.table(annotationMelange$TOCSY$liste_resultat, file = argLs[["annotationTOCSY"]], quote = FALSE,
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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285 row.names = FALSE, sep = "\t")
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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286 if (nrow(annotationMelange$TOCSY$listing_ppm_commun) != 0)
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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287 write.table(annotationMelange$TOCSY$listing_ppm_commun, file = argLs[["ppmCommunTOCSY"]], quote = FALSE,
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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288 row.names = FALSE, sep = "\t")
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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289 }
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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290
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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291 ## Combinaison de sequences
3
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292 if (cosy + jres + hmbc + hsqc + tocsy > 1) {
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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293 write.table(annotationMelange$combination, file = argLs[["annotationCombination"]], quote = FALSE,
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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294 row.names = FALSE, sep = "\t")
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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295 }
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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296 st1 <- Sys.time()
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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297 print(st1 - st0)
2
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298
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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299 ## Ending
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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300 ##--------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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301 cat("\nEnd of '2D NMR annotation' Galaxy module call: ", as.character(Sys.time()), sep = "")
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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302 sink()
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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303 options(stringsAsFactors = strAsFacL)
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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304 rm(list = ls())