Mercurial > repos > melpetera > batchcorrection

comparison BC/batch_correction_docker_wrapper.R @ 4:23314e1192d4 draft default tip

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author melpetera
date Thu, 14 Jan 2021 09:56:58 +0000
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3:73892ef177e3 4:23314e1192d4
1 #!/usr/bin/env Rscript
2
3 ################################################################################################
4 # batch_correction_main_wrapper #
5 # #
6 # Author: Nils Paulhe #
7 # User: Galaxy #
8 # Original data: -- #
9 # Starting date: 2017-12-11 #
10 # Version 1: 2017-12-11 #
11 # #
12 # #
13 # #
14 ################################################################################################
15
16 library(batch) #necessary for parseCommandArgs function
17
18 ##------------------------------
19 ## init. prog. constants
20 ##------------------------------
21
22 argv.wrapper <- commandArgs(trailingOnly = FALSE)
23 script.path <- sub("--file=", "", argv.wrapper[grep("--file=", argv.wrapper)])
24 prog.name <- basename(script.path)
25
26 ##------------------------------
27 ## init. functions
28 ##------------------------------
29
30 script_bypass <- function(other.script.name) {
31 initial.options <- commandArgs(trailingOnly = FALSE)
32 file.arg.name <- "--file="
33 script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
34 script.basename <- dirname(script.name)
35 other.script.fullpath <- paste(sep="/", script.basename, other.script.name)
36 other.script.cmd <- paste(sep=" ", "Rscript", other.script.fullpath, "-h")
37 system(other.script.cmd, wait=TRUE)
38 }
39
40 source_wrapper <- function(other.script.name){
41 initial.options <- commandArgs(trailingOnly = FALSE)
42 file.arg.name <- "--file="
43 script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
44 script.basename <- dirname(script.name)
45 other.script.fullpath <- paste(sep="/", script.basename, other.script.name)
46 source(other.script.fullpath)
47 }
48
49 ##------------------------------
50 ## Test Help
51 ##------------------------------
52
53 if (length(grep('-h', argv.wrapper)) > 0) {
54 cat("Usage: Rscript ",
55 prog.name,
56 "{args} \n",
57 "parameters: \n",
58 "\t-h: display this help message, call all scripts with the same option and exit (optional) \n",
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",
60 "for other parameters, please refer to each script specific options and parameters. \n",
61 "\n")
62 script_bypass("batch_correction_all_loess_wrapper.R")
63 script_bypass("batch_correction_wrapper.R")
64 quit(status = 0)
65 }
66
67 ##------------------------------
68 ## check if loess or normal
69 ##------------------------------
70
71 if (length(grep('--loess', argv.wrapper)) > 0) {
72 source_wrapper("batch_correction_all_loess_wrapper.R")
73 } else {
74 source_wrapper("batch_correction_3Lwrapper.R")
75 }
76