Mercurial > repos > ethevenot > checkformat
annotate checkformat_wrapper.R @ 2:b6a6b4cc932a draft
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
author | ethevenot |
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date | Tue, 06 Jun 2017 11:51:33 -0400 |
parents | e194eec8e70c |
children | 80a38d36f946 |
rev | line source |
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1
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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1 #!/usr/bin/env Rscript |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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2 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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3 library(batch) ## parseCommandArgs |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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4 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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5 source_local <- function(fname){ |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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6 argv <- commandArgs(trailingOnly = FALSE) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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7 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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8 source(paste(base_dir, fname, sep="/")) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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9 } |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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10 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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11 source_local("checkformat_script.R") |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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12 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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13 argVc <- unlist(parseCommandArgs(evaluate = FALSE)) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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14 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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15 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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16 ##------------------------------ |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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17 ## Initializing |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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18 ##------------------------------ |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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19 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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20 ## options |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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21 ##-------- |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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22 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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23 strAsFacL <- options()$stringsAsFactors |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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24 options(stringsAsFactors = FALSE) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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25 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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26 ## constants |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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27 ##---------- |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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28 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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29 modNamC <- "Check Format" ## module name |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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30 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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31 ## log file |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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32 ##--------- |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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33 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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34 sink(argVc["information"]) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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35 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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36 cat("\nStart of the '", modNamC, "' Galaxy module call: ", |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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37 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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38 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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39 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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40 ##------------------------------ |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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41 ## Computation |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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42 ##------------------------------ |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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43 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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44 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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45 resLs <- readAndCheckF(argVc["dataMatrix_in"], |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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46 argVc["sampleMetadata_in"], |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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47 argVc["variableMetadata_in"]) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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48 chkL <- resLs[["chkL"]] |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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49 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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50 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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51 ##------------------------------ |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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52 ## Ending |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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53 ##------------------------------ |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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54 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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55 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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56 if(chkL) { |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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57 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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58 cat("\nTable formats are OK; enjoy your analyses!\n", sep="") |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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59 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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60 cat("\nEnd of the '", modNamC, "' Galaxy module call: ", |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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61 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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62 |
2
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
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63 cat("\n\n\n============================================================================") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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64 cat("\nAdditional information about the call:\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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65 cat("\n1) Parameters:\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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66 print(cbind(value = argVc)) |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
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67 |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
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68 cat("\n2) Session Info:\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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69 sessioninfo <- sessionInfo() |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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70 cat(sessioninfo$R.version$version.string,"\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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71 cat("Main packages:\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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72 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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73 cat("Other loaded packages:\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
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74 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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75 |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
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76 cat("============================================================================\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
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77 |
1
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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78 sink() |
2
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
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79 |
1
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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80 } else { |
2
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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81 |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
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82 cat("\n\n\n============================================================================") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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83 cat("\nAdditional information about the call:\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
1
diff
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84 cat("\n1) Parameters:\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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85 print(cbind(value = argVc)) |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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86 |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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87 cat("\n2) Session Info:\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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88 sessioninfo <- sessionInfo() |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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89 cat(sessioninfo$R.version$version.string,"\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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90 cat("Main packages:\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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91 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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92 cat("Other loaded packages:\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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93 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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94 |
b6a6b4cc932a
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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95 cat("============================================================================\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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96 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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97 sink() |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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98 stop("Please check the generated 'information' file") |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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99 |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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100 } |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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101 |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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102 ## closing |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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103 ##-------- |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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104 |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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105 options(stringsAsFactors = strAsFacL) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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106 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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107 rm(list = ls()) |