Mercurial > repos > eschen42 > w4mcorcov
annotate w4mcorcov_wrapper.R @ 6:7bd523ca1f9a draft
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
author | eschen42 |
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date | Wed, 18 Jul 2018 12:35:55 -0400 |
parents | 50f60f94c034 |
children | 342570ad880c |
rev | line source |
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0
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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1 #!/usr/bin/env Rscript |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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2 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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3 # This script assumes that it is being executed in a current working directory containing the following files: |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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4 # - w4mcorcov_lib.R |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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5 # - w4mcorcov_input.R |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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6 # - w4mcorcov_calc.R |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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7 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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8 ## constants |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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9 ##---------- |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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10 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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11 modNamC <- "w4mcorcov" ## module name |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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12 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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13 topEnvC <- environment() |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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14 nl <- "\n" |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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15 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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16 ## options |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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17 ##-------- |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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18 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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19 strAsFacL <- options()$stringsAsFactors |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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20 options(stringsAsFactors = FALSE) |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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21 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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22 ## subroutines |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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23 ##---------- |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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24 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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25 source("w4mcorcov_lib.R") |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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26 source("w4mcorcov_util.R") |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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27 source("w4mcorcov_input.R") |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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28 source("w4mcorcov_salience.R") |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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29 source("w4mcorcov_calc.R") |
23f9fad4edfc
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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30 source("w4mcorcov_output.R") |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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31 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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32 ## log file |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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33 ##--------- |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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34 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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35 my_log <- function(x, ...) { cat(paste(iso8601.znow(), " ", x, ..., nl, sep=""))} |
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7bd523ca1f9a
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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36 my_fatal <- function(x, ...) { |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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37 my_log("ERROR: ", x, ...) |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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38 quit(save = "no", status = 11, runLast = TRUE) |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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39 } |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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40 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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41 my_log("Start of the '", modNamC, "' Galaxy module call: ") |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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42 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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43 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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44 ######## |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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45 # MAIN # |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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46 ######## |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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47 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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48 argVc <- unlist(parseCommandArgs(evaluate=FALSE)) |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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49 my_env <- new.env() |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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50 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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51 ##------------------------------ |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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52 ## Initializing |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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53 ##------------------------------ |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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54 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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55 ## arguments |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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56 ##---------- |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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57 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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58 # files |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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59 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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60 my_env$dataMatrix_in <- as.character(argVc["dataMatrix_in"]) |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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61 my_env$sampleMetadata_in <- as.character(argVc["sampleMetadata_in"]) |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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62 my_env$variableMetadata_in <- as.character(argVc["variableMetadata_in"]) |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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63 my_env$contrast_detail <- as.character(argVc["contrast_detail"]) |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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64 my_env$contrast_corcov <- as.character(argVc["contrast_corcov"]) |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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65 my_env$contrast_salience <- as.character(argVc["contrast_salience"]) |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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66 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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67 # other parameters |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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68 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582
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69 my_env$tesC <- as.character(argVc["tesC"]) |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582
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70 my_env$facC <- as.character(argVc["facC"]) |
e03582f26617
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582
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71 my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"]) |
e03582f26617
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582
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72 my_env$levCSV <- as.character(argVc["levCSV"]) |
e03582f26617
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582
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73 my_env$matchingC <- as.character(argVc["matchingC"]) |
e03582f26617
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582
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74 my_env$labelFeatures <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL' |
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7bd523ca1f9a
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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75 my_env$cplot_o <- as.logical(argVc["cplot_o"]) # TRUE if orthogonal C-plot is requested |
7bd523ca1f9a
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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76 my_env$cplot_p <- as.logical(argVc["cplot_p"]) # TRUE if parallel C-plot is requested |
7bd523ca1f9a
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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77 my_env$cplot_y <- as.character(argVc["cplot_y"]) # Choice of covariance/correlation for Y-axis on C-plot |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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78 |
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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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79 label_features <- my_env$labelFeatures |
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80 labelfeatures_check <- TRUE |
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81 if ( is.na(label_features) ) { |
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82 labelfeatures_check <- FALSE |
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83 } else if ( is.null(label_features) ) { |
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84 labelfeatures_check <- FALSE |
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85 } else if (label_features != "ALL") { |
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86 if ( is.na(as.numeric(label_features)) ) |
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87 labelfeatures_check <- FALSE |
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88 else if ( as.numeric(label_features) < 0 ) |
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89 labelfeatures_check <- FALSE |
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90 } |
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91 if ( !labelfeatures_check ) { |
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92 my_log("invalid argument: labelFeatures") |
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93 print(label_features) |
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94 quit(save = "no", status = 10, runLast = TRUE) |
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95 } |
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96 |
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97 corcov_tsv_colnames <- TRUE |
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98 corcov_tsv_append <- FALSE |
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99 corcov_tsv_action <- function(tsv) { |
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100 tsv_action_factory( |
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101 file = my_env$contrast_corcov |
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102 , colnames = corcov_tsv_colnames |
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103 , append = corcov_tsv_append |
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104 )(tsv) |
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105 corcov_tsv_colnames <<- FALSE |
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106 corcov_tsv_append <<- TRUE |
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107 } |
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108 |
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109 salience_tsv_colnames <- TRUE |
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110 salience_tsv_append <- FALSE |
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111 salience_tsv_action <- function(tsv) { |
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112 tsv_action_factory( |
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113 file = my_env$contrast_salience |
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114 , colnames = salience_tsv_colnames |
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115 , append = salience_tsv_append |
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116 )(tsv) |
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117 salience_tsv_colnames <<- FALSE |
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118 salience_tsv_append <<- TRUE |
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119 } |
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120 |
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121 my_log( "-------------------------- Reading input data --------------------------") |
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122 |
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123 # read_inputs is defined in w4mcorcov_input.R |
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124 my_result <- read_inputs(input_env = my_env, failure_action = my_log) |
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125 |
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126 if ( is.logical(my_result) && my_result) { |
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127 my_log( "-------------------------- Beginning data processing --------------------------") |
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128 |
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129 # receiver for result of the call to corcov_calc |
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130 my_result <- NULL |
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131 |
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132 # compute and plot the correlation_vs_covariance details plot |
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133 # The parameter settings here are generally taken from bioconductor ropls::plot.opls source. |
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134 if ( my_env$cplot_p || my_env$cplot_o ) { |
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135 old_par <- par( |
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136 font = 2 # bold font face |
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137 , font.axis = 2 # bold font face for axis |
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138 , font.lab = 2 # bold font face for x and y labels |
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139 , lwd = 2 # line-width - interpretation is device spcific |
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140 , pch = 18 # black diamond plot-character, see help for graphics::points |
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141 , pty = "m" # do not force plots to be square |
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142 , no.readonly = TRUE # only save writable parameters |
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143 ) |
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144 pdf_height <- 12 |
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145 pdf_width <- 8 |
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146 my_layout <- function() { |
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147 # lay out 2 columns by 3 rows with extra width at the margin of individual plots |
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148 layout( |
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149 matrix( |
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150 # blank row plot 1 & 2 blank row plot 3 & 4 blank row plot 5 & 6 blank row |
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151 c(0,0,0,0,0, 0,1,0,2,0, 0,0,0,0,0, 0,3,0,4,0, 0,0,0,0,0, 0,5,0,6,0, 0,0,0,0,0) |
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152 , nrow = 7 |
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153 , ncol = 5 |
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154 , byrow = TRUE |
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155 ) |
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156 # slim columns 1, 3, and 5 |
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157 , widths = c(0.1, 0.9, 0.1, 0.9, 0.1) |
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158 # slim rows 1, 3, 5, and 7 |
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159 , heights = c(0.1, 0.9, 0.1, 0.9, 0.1, 0.9, 0.1) |
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160 ) |
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161 } |
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162 } else { |
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163 old_par <- par( |
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164 font = 2 # bold font face |
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165 , font.axis = 2 # bold font face for axis |
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166 , font.lab = 2 # bold font face for x and y labels |
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167 , lwd = 2 # line-width - interpretation is device spcific |
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168 , pch = 18 # black diamond plot-character, see help for graphics::points |
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169 , pty = "m" # do not force plots to be square |
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170 , no.readonly = TRUE # only save writable parameters |
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171 ) |
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172 pdf_height <- 8 |
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173 pdf_width <- 8 |
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174 my_layout <- function() { |
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175 # lay out 2 columns by 2 rows with extra width at the margin of individual plots |
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176 layout( |
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177 matrix( |
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178 # blank row plot 1 & 2 blank row plot 3 & 4 blank row |
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179 c(0,0,0,0,0, 0,1,0,2,0, 0,0,0,0,0, 0,3,0,4,0, 0,0,0,0,0) |
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180 , nrow = 5 |
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181 , ncol = 5 |
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182 , byrow = TRUE |
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183 ) |
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184 # slim columns 1, 3, and 5 |
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185 , widths = c(0.1, 0.9, 0.1, 0.9, 0.1) |
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186 # slim rows 1, 3, and 5 |
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187 , heights = c(0.1, 0.9, 0.1, 0.9, 0.1) |
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188 ) |
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189 } |
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190 } |
0
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191 plot2pdf( |
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192 file.name = my_env$contrast_detail |
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193 , width = pdf_width |
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194 , height = pdf_height |
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195 , plot.function = function() { |
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196 # plot layout four or six plots per page |
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197 my_layout() |
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198 my_result <<- corcov_calc( |
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199 calc_env = my_env |
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200 , failure_action = my_fatal |
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201 , progress_action = my_log |
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202 , corcov_tsv_action = corcov_tsv_action |
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203 , salience_tsv_action = salience_tsv_action |
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204 ) |
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205 } |
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206 ) |
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207 par(old_par) |
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208 |
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209 my_log( "-------------------------- Finished data processing --------------------------") |
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210 } |
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211 |
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212 my_log( "End of the '", modNamC, "' Galaxy module call") |
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213 |
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214 if (is.logical(my_result) && my_result) { |
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215 quit(save = "no", status = 0, runLast = TRUE) |
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216 } else { |
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217 my_log("failure :(") |
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218 quit(save = "no", status = 10, runLast = TRUE) |
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219 } |