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66
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1 #! /usr/bin/Rscript
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74
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2 ins_check_run <- function() {
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3 if ("mzID" %in% rownames(installed.packages())){}
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4 else {
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5 source("https://bioconductor.org/biocLite.R")
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6 biocLite('mzID')
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7 }
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8 if ('dplyr' %in% rownames(installed.packages())){}
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9 else {
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10 install.packages('dplyr', repos='http://cran.us.r-project.org')
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11 }
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12 }
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13
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14 ins_check_run()
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66
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15 args <- commandArgs(trailingOnly = TRUE)
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16 #source("https://bioconductor.org/biocLite.R")
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17 #biocLite("mzID")
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18 library(mzID)
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19 library(dplyr)
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20 mzResults <- mzID(args[1])
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21 flatresults <- flatten(mzResults)
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22 write.table(flatresults,"flat_mzIdentML.txt",sep="\t",quote=FALSE,row.names=FALSE) |
