Mercurial > repos > lecorguille > xcms_merge

annotate xcms_merge.r @ 18:9128f47ffd12 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty
author lecorguille
date Thu, 04 Oct 2018 09:48:26 -0400
parents 40791ab6c06b
children 068243731881
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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1 #!/usr/bin/env Rscript
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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3 #Import the different functions
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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4 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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5 source_local("lib.r")
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40791ab6c06b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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6 source_local("lib-xcms3.x.x.r")
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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8 pkgs <- c("xcms","batch")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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9 loadAndDisplayPackages(pkgs)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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10 cat("\n\n");
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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12 args <- parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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15 cat("\tXSET MERGING...\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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17 mergeXDataReturn <- mergeXData(args)
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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18 xdata <- mergeXDataReturn$xdata
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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19 singlefile <- mergeXDataReturn$singlefile
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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20 md5sumList <- mergeXDataReturn$md5sumList
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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21 sampleNamesList <- mergeXDataReturn$sampleNamesList
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lecorguille
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22 chromTIC <- mergeXDataReturn$chromTIC
2d27c70635eb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 317a00e08b72961bc7df134ebf4001fb783858a6
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23 chromBPI <- mergeXDataReturn$chromBPI
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25 # Create a sampleMetada file
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26 sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")
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28 cat("\n\n")
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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30 cat("\tXCMSnExp OBJECT INFO\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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31 print(pData(xdata))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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32 print(xdata)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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33 cat("\n\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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35 cat("\txcmsSet OBJECT INFO\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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36 # Get the legacy xcmsSet object
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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37 xset <- getxcmsSetObject(xdata)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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38 print(xset@phenoData)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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39 print(xset)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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40 cat("\n\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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42 cat("\tSAVE RData\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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43 #saving R data in .Rdata file to save the variables used in the present tool
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44 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList", "chromTIC", "chromBPI")
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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45 save(list=objects2save[objects2save %in% ls()], file="merged.RData")