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1 #!/usr/bin/env Rscript
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2
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3 ################################################################################################
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4 # batch_correction_main_wrapper #
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5 # #
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6 # Author: Nils Paulhe #
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7 # User: Galaxy #
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8 # Original data: -- #
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9 # Starting date: 2017-12-11 #
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10 # Version 1: 2017-12-11 #
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11 # #
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12 # #
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13 # #
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14 ################################################################################################
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15
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16 library(batch) #necessary for parseCommandArgs function
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17
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18 ##------------------------------
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19 ## init. prog. constants
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20 ##------------------------------
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21
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22 argv.wrapper <- commandArgs(trailingOnly = FALSE)
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23 script.path <- sub("--file=", "", argv.wrapper[grep("--file=", argv.wrapper)])
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24 prog.name <- basename(script.path)
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25
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26 ##------------------------------
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27 ## init. functions
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28 ##------------------------------
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29
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30 script_bypass <- function(other.script.name) {
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31 initial.options <- commandArgs(trailingOnly = FALSE)
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32 file.arg.name <- "--file="
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33 script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
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34 script.basename <- dirname(script.name)
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35 other.script.fullpath <- paste(sep="/", script.basename, other.script.name)
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36 other.script.cmd <- paste(sep=" ", "Rscript", other.script.fullpath, "-h")
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37 system(other.script.cmd, wait=TRUE)
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38 }
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39
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40 source_wrapper <- function(other.script.name){
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41 initial.options <- commandArgs(trailingOnly = FALSE)
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42 file.arg.name <- "--file="
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43 script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
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44 script.basename <- dirname(script.name)
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45 other.script.fullpath <- paste(sep="/", script.basename, other.script.name)
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46 source(other.script.fullpath)
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47 }
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48
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49 ##------------------------------
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50 ## Test Help
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51 ##------------------------------
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52
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53 if (length(grep('-h', argv.wrapper)) > 0) {
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54 cat("Usage: Rscript ",
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55 prog.name,
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56 "{args} \n",
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57 "parameters: \n",
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58 "\t-h: display this help message, call all scripts with the same option and exit (optional) \n",
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59 "\t--loess \"TRUE\": call the script as \"batch_correction_all_loess_wrapper.R\"; otherwise call it as \"batch_correction_wrapper.R\" one (optional) \n",
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60 "for other parameters, please refer to each script specific options and parameters. \n",
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61 "\n")
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62 script_bypass("batch_correction_all_loess_wrapper.R")
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63 script_bypass("batch_correction_wrapper.R")
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64 quit(status = 0)
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65 }
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66
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67 ##------------------------------
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68 ## check if loess or normal
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69 ##------------------------------
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70
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71 if (length(grep('--loess', argv.wrapper)) > 0) {
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72 source_wrapper("batch_correction_all_loess_wrapper.R")
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73 } else {
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74 source_wrapper("batch_correction_wrapper.R")
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75 }
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76
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