diff univariate_wrapper.R @ 4:3017385625f6 draft

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
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line diff
--- a/univariate_wrapper.R	Sun Oct 30 14:17:09 2016 -0400
+++ b/univariate_wrapper.R	Thu Jan 11 10:21:17 2018 -0500
@@ -2,6 +2,28 @@
 
 library(batch) ## parseCommandArgs
 
+# Constants
+argv <- commandArgs(trailingOnly = FALSE)
+script.path <- sub("--file=","",argv[grep("--file=",argv)])
+prog.name <- basename(script.path)
+
+# Print help
+if (length(grep('-h', argv)) >0) {
+	cat("Usage:", prog.name,
+	    "dataMatrix_in myDataMatrix.tsv",
+	    "sampleMetadata_in mySampleData.tsv",
+	    "variableMetadata_in myVariableMetadata.tsv",
+	    "facC qual",
+	    "tesC kruskal",
+	    "adjC fdr",
+	    "thrN 0.05",
+	    "variableMetadata_out myVariableMetadata_out.tsv",
+	    "figure figure.pdf",
+	    "information information.txt",
+		"\n")
+	quit(status = 0)
+}
+
 source_local <- function(fname){
     argv <- commandArgs(trailingOnly = FALSE)
     base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
@@ -146,6 +168,21 @@
 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
     as.character(Sys.time()), "\n", sep = "")
 
+cat("\n\n\n============================================================================")
+cat("\nAdditional information about the call:\n")
+cat("\n1) Parameters:\n")
+print(cbind(value = argVc))
+
+cat("\n2) Session Info:\n")
+sessioninfo <- sessionInfo()
+cat(sessioninfo$R.version$version.string,"\n")
+cat("Main packages:\n")
+for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+cat("Other loaded packages:\n")
+for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+
+cat("============================================================================\n")
+
 sink()
 
 options(stringsAsFactors = strAsFacL)