annotate qualitymetrics_wrapper.R @ 3:acdf51018708 draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit b7e47e59ea753fe9f73f2b83bcaae895b21269f6
author ethevenot
date Wed, 28 Feb 2018 09:32:42 -0500
parents b4f5b5bc01dd
children
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
ethevenot
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1 #!/usr/bin/Rscript --vanilla --slave --no-site-file
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
ethevenot
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3 ################################################################################################
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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4 # WRAPPER FOR QC_script.R (ANALYSES FOR QUALITY CONTROL) #
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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5 # #
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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6 # Author: Melanie PETERA based on Marion LANDI's filters' wrapper #
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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7 # User: Galaxy #
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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8 # Original data: used with QC_script.R #
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
ethevenot
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9 # Starting date: 04-09-2014 #
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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10 # V-1: Restriction of old filter wrapper to quality control (CV) #
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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11 # #
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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12 # #
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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13 # Input files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt #
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
ethevenot
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14 # Output files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt #
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
ethevenot
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15 # #
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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16 ################################################################################################
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
ethevenot
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19 library(batch) #necessary for parseCommandArgs function
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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20 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
ethevenot
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22 source_local <- function(...){
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
ethevenot
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23 argv <- commandArgs(trailingOnly = FALSE)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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24 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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25 for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))}
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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26 }
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
ethevenot
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27 #Import the different functions
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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28 source_local("qualitymetrics_script.R", "easyrlibrary-lib/RcheckLibrary.R", "easyrlibrary-lib/miniTools.R")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
ethevenot
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31 suppressMessages(library(ropls)) ## to be used in qualityMetricsF
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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33 if(packageVersion("ropls") < "1.4.0")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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34 stop("Please use 'ropls' versions of 1.4.0 and above")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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36 if(length(args) < 9){ stop("NOT enough arguments !!!") }
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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38 args$Compa <- as.logical(args$Compa)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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39 args$poolAsPool1L <- as.logical(args$poolAsPool1L)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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41 QualityControl(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in,
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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42 args$CV, args$Compa, args$seuil, args$poolAsPool1L,
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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43 args$dataMatrix_out, args$sampleMetadata_out, args$variableMetadata_out, args$figure, args$information)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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45 #QualityControl(ion.file.in, meta.samp.file.in, meta.ion.file.in,
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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46 # CV, Compa, seuil,
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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47 # ion.file.out, meta.samp.file.out, meta.ion.file.out)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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49 #delete the parameters to avoid the passage to the next tool in .RData image
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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50 rm(args)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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