Mercurial > repos > ethevenot > profia
annotate profia_wrapper.R @ 0:39ccace77270 draft
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
author | ethevenot |
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date | Sun, 26 Mar 2017 17:37:12 -0400 |
parents | |
children | 4753e64cf694 |
rev | line source |
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0
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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changeset
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1 #!/usr/bin/env Rscript |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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2 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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3 library(batch) ## parseCommandArgs |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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4 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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5 argVc <- unlist(parseCommandArgs(evaluate=FALSE)) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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6 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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7 ##------------------------------ |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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8 ## Initializing |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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9 ##------------------------------ |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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10 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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11 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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changeset
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12 ## libraries |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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13 ##---------- |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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14 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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15 suppressMessages(library(proFIA)) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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16 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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17 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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18 ## constants |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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19 ##---------- |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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20 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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changeset
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21 modNamC <- "proFIA" ## module name |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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22 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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23 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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24 ## log file |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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25 ##--------- |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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26 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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changeset
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27 sink(argVc["information"]) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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28 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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changeset
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29 cat("\nStart of the '", modNamC, "' Galaxy module call: ", |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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changeset
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30 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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31 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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changeset
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32 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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changeset
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33 ## arguments |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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34 ##---------- |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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35 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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changeset
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36 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff
changeset
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37 if("zipfile" %in% names(argVc)) { |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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38 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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changeset
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39 zipfile <- argVc["zipfile"] |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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40 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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41 ## We unzip automatically the raw files from the zip file |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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42 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff
changeset
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43 if(exists("zipfile") && (zipfile!="")) { |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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changeset
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44 if(!file.exists(zipfile)){ |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff
changeset
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45 error_message=paste("Cannot access the Zip file:", zipfile) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff
changeset
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46 print(error_message) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff
changeset
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47 stop(error_message) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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changeset
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48 } |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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49 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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changeset
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50 ## unzip |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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51 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff
changeset
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52 suppressWarnings(unzip(zipfile, unzip="unzip")) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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53 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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changeset
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54 ## get the directory name |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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55 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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changeset
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56 filesInZip=unzip(zipfile, list=T); |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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57 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))); |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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58 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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59 directory = "." |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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60 if (length(directories) == 1) directory = directories |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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61 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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62 cat("files_root_directory\t",directory,"\n") |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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63 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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64 } |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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65 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff
changeset
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66 } else if ("library" %in% names(argVc)) { |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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67 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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68 directory <- argVc["library"] |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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69 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff
changeset
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70 if(!file.exists(directory)) { |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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71 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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72 error_message=paste("Cannot access the directory:", directory,". Please check that the directory really exists.") |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff
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73 print(error_message) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff
changeset
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74 stop(error_message) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff
changeset
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75 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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76 } |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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77 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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78 } else { |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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79 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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80 error_message <- "No zipfile nor input library available" |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff
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81 print(error_message) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff
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82 stop(error_message) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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83 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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84 } |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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85 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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86 ##------------------------------ |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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87 ## Computations |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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88 ##------------------------------ |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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89 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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90 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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91 optWrnN <- options()$warn |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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92 options(warn = -1) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff
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93 |
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94 stpI <- 1 |
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95 |
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96 cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "") |
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97 |
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98 fiaset <- proFIAset(directory, |
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99 ppm = as.numeric(argVc["ppmN"]), |
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100 parallel = FALSE) |
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101 |
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102 stpI <- stpI + 1 |
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103 |
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104 cat("\n", stpI, ") Peak alignment ('group.FIA'):\n", sep = "") |
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105 |
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106 fiaset <- group.FIA(fiaset, |
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107 ppmGroup = as.numeric(argVc["ppmGroupN"]), |
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108 fracGroup = as.numeric(argVc["fracGroupN"])) |
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109 |
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110 stpI <- stpI + 1 |
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111 |
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112 cat("\n", stpI, ") Creating the peak table ('makeDataMatrix'):\n", sep = "") |
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113 |
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114 fiaset <- makeDataMatrix(fiaset, |
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115 maxo = FALSE) |
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116 |
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117 stpI <- stpI + 1 |
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118 |
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119 kI <- as.integer(argVc["kI"]) |
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120 |
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121 if(kI > 0) { |
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122 |
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123 cat("\n", stpI, ") Imputing missing values ('imputeMissingValues.WKNN_TN'):\n", sep = "") |
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124 |
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125 fiaset <- imputeMissingValues.WKNN_TN(fiaset, |
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126 k = kI) |
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127 |
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128 stpI <- stpI + 1 |
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129 } |
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130 |
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131 options(warn = optWrnN) |
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132 |
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133 |
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134 ##------------------------------ |
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135 ## Ending |
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136 ##------------------------------ |
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137 |
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138 |
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139 ## Plotting |
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140 ##--------- |
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141 |
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142 cat("\n", stpI, ") Plotting ('plot'):\n", sep = "") |
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143 |
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144 pdf(argVc["figure"]) |
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145 |
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146 plot(fiaset) |
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147 |
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148 dev.off() |
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149 |
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150 stpI <- stpI + 1 |
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151 |
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152 ## Printing |
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153 ##--------- |
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154 |
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155 cat("\n", stpI, ") Printing ('show'):\n", sep = "") |
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156 |
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157 fiaset |
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158 |
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159 stpI <- stpI + 1 |
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160 |
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161 ## Exporting |
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162 ##---------- |
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163 |
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164 cat("\n", stpI, ") Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'):\n", sep = "") |
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165 |
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166 datMN <- exportDataMatrix(fiaset) |
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167 samDF <- exportSampleMetadata(fiaset) |
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168 varDF <- exportVariableMetadata(fiaset) |
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169 |
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170 if(nrow(datMN) == nrow(samDF) && ncol(datMN) == nrow(varDF)) { |
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171 datDF <- as.data.frame(t(datMN)) |
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172 } else { |
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173 datDF <- as.data.frame(datMN) |
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174 } |
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175 rownames(varDF) <- rownames(datDF) |
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176 |
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177 datDF <- cbind.data.frame(dataMatrix = rownames(datDF), |
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178 datDF) |
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179 write.table(datDF, |
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180 file = argVc["dataMatrix_out"], |
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181 quote = FALSE, |
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182 row.names = FALSE, |
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183 sep = "\t") |
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184 |
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185 samDF <- cbind.data.frame(sampleMetadata = rownames(samDF), |
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186 samDF) |
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187 write.table(samDF, |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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188 file = argVc["sampleMetadata_out"], |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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189 quote = FALSE, |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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190 row.names = FALSE, |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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191 sep = "\t") |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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192 |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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193 varDF <- cbind.data.frame(variableMetadata = rownames(varDF), |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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194 varDF) |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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195 write.table(varDF, |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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196 file = argVc["variableMetadata_out"], |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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197 quote = FALSE, |
39ccace77270
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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198 row.names = FALSE, |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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199 sep = "\t") |
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200 |
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201 |
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202 ## Closing |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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203 ##-------- |
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204 |
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205 cat("\nEnd of '", modNamC, "' Galaxy module call: ", |
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206 as.character(Sys.time()), "\n", sep = "") |
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207 |
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208 sink() |
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209 |
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210 rm(list = ls()) |