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comparison univariate_wrapper.R @ 4:3017385625f6 draft

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planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
author ethevenot
date Thu, 11 Jan 2018 10:21:17 -0500
parents 140290de7986
children
comparison
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3:140290de7986 4:3017385625f6
1 #!/usr/bin/env Rscript 1 #!/usr/bin/env Rscript
2 2
3 library(batch) ## parseCommandArgs 3 library(batch) ## parseCommandArgs
4
5 # Constants
6 argv <- commandArgs(trailingOnly = FALSE)
7 script.path <- sub("--file=","",argv[grep("--file=",argv)])
8 prog.name <- basename(script.path)
9
10 # Print help
11 if (length(grep('-h', argv)) >0) {
12 cat("Usage:", prog.name,
13 "dataMatrix_in myDataMatrix.tsv",
14 "sampleMetadata_in mySampleData.tsv",
15 "variableMetadata_in myVariableMetadata.tsv",
16 "facC qual",
17 "tesC kruskal",
18 "adjC fdr",
19 "thrN 0.05",
20 "variableMetadata_out myVariableMetadata_out.tsv",
21 "figure figure.pdf",
22 "information information.txt",
23 "\n")
24 quit(status = 0)
25 }
4 26
5 source_local <- function(fname){ 27 source_local <- function(fname){
6 argv <- commandArgs(trailingOnly = FALSE) 28 argv <- commandArgs(trailingOnly = FALSE)
7 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) 29 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
8 source(paste(base_dir, fname, sep="/")) 30 source(paste(base_dir, fname, sep="/"))
144 ##-------- 166 ##--------
145 167
146 cat("\nEnd of '", modNamC, "' Galaxy module call: ", 168 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
147 as.character(Sys.time()), "\n", sep = "") 169 as.character(Sys.time()), "\n", sep = "")
148 170
171 cat("\n\n\n============================================================================")
172 cat("\nAdditional information about the call:\n")
173 cat("\n1) Parameters:\n")
174 print(cbind(value = argVc))
175
176 cat("\n2) Session Info:\n")
177 sessioninfo <- sessionInfo()
178 cat(sessioninfo$R.version$version.string,"\n")
179 cat("Main packages:\n")
180 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
181 cat("Other loaded packages:\n")
182 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
183
184 cat("============================================================================\n")
185
149 sink() 186 sink()
150 187
151 options(stringsAsFactors = strAsFacL) 188 options(stringsAsFactors = strAsFacL)
152 189
153 rm(list = ls()) 190 rm(list = ls())