Mercurial > repos > ethevenot > univariate
comparison univariate_wrapper.R @ 4:3017385625f6 draft
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
author | ethevenot |
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date | Thu, 11 Jan 2018 10:21:17 -0500 |
parents | 140290de7986 |
children |
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3:140290de7986 | 4:3017385625f6 |
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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()) |