Mercurial > repos > workflow4metabolomics > camera_combinexsannos

annotate CAMERA_combinexsAnnos.r @ 3:3bf04fc404d9 draft

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"planemo upload commit e363c270e2f9d72cb0ede1a7f3bc61418b72c4c4"
author workflow4metabolomics
date Mon, 30 Mar 2020 10:21:30 -0400
parents 139ff66b0b5d
children 4c4945bce185
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1 #!/usr/bin/env Rscript
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3 # ----- PACKAGE -----
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4 cat("\tSESSION INFO\n")
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6 #Import the different functions
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7 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
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8 source_local("lib.r")
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10 pkgs=c("CAMERA","multtest","batch")
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11 loadAndDisplayPackages(pkgs)
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12 cat("\n\n");
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14 # ----- ARGUMENTS -----
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15 cat("\tARGUMENTS INFO\n")
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17 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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18 write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
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20 cat("\n\n");
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23 # ----- PROCESSING INFILE -----
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24 cat("\tINFILE PROCESSING INFO\n")
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26 #image is an .RData file necessary to use xset variable given by previous tools
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27 load(args$image_pos)
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28 xaP=xa
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30 diffrepP=NULL
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31 if (exists("diffrep")) diffrepP=diffrep
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33 load(args$image_neg)
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34 xaN=xa
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36 diffrepN=NULL
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37 if (exists("diffrep")) diffrepN=diffrep
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40 cat("\n\n")
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43 # ----- ARGUMENTS PROCESSING -----
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44 cat("\tARGUMENTS PROCESSING INFO\n")
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46 # Save arguments to generate a report
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47 if (!exists("listOFargs")) listOFargs=list()
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48 listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_combinexsAnnos")]] = args
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50 cat("\n\n")
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53 # ----- PROCESSING INFO -----
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54 cat("\tMAIN PROCESSING INFO\n")
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56 cAnnot=combinexsAnnos_function(
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57 xaP=xaP,xaN=xaN,
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58 diffrepP=diffrepP, diffrepN=diffrepN,
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59 pos=args$pos, tol=args$tol,ruleset=args$ruleset, keep_meta=args$keep_meta,
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60 convertRTMinute=args$convertRTMinute, numDigitsMZ=args$numDigitsMZ, numDigitsRT=args$numDigitsRT,
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61 variableMetadataOutput="variableMetadata.tsv"
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62 )
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64 # ----- EXPORT -----
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65
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66 #saving R data in .Rdata file to save the variables used in the present tool
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67 objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFargs","zipfile","singlefile")
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68 save(list=objects2save[objects2save %in% ls()], file="combinexsAnnos.RData")
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69
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70 cat("\n\n")
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72 cat("\tDONE\n")