Mercurial > repos > ethevenot > checkformat
annotate checkformat_wrapper.R @ 1:e194eec8e70c draft
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
author | ethevenot |
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date | Sat, 06 Aug 2016 11:54:28 -0400 |
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children | b6a6b4cc932a |
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
parents:
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2 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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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
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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
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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
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10 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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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
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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
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26 ## constants |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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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
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29 modNamC <- "Check Format" ## module name |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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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
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32 ##--------- |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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33 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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34 sink(argVc["information"]) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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35 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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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
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40 ##------------------------------ |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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41 ## Computation |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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42 ##------------------------------ |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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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
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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
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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
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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
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56 if(chkL) { |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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57 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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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
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59 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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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
ethevenot
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62 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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63 sink() |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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64 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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65 } else { |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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66 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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67 sink() |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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68 stop("Please check the generated 'information' file") |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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69 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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70 } |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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71 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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72 ## closing |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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73 ##-------- |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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74 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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75 options(stringsAsFactors = strAsFacL) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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76 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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77 rm(list = ls()) |