# HG changeset patch
# User iuc
# Date 1591874297 14400
# Node ID 2b80a25960646c7ce3ee0246f174a2b17ae05c32
# Parent  704c401e0afbee34765a7b3ce789bdebbeb5b5c7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit 8007f71281553ddfa45e6f8e1172952d956bb000"

diff -r 704c401e0afb -r 2b80a2596064 bum.R
--- a/bum.R	Thu Jan 23 14:07:54 2020 -0500
+++ b/bum.R	Thu Jun 11 07:18:17 2020 -0400
@@ -2,15 +2,16 @@
 # Usage: Rscript bum.R --input p-values.txt --output result.txt --verbose TRUE
 
 # Set up R error handling to go to stderr
-options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
-
-# Avoid crashing Galaxy with an UTF8 error on German LC settings
-#loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+err_foo <- function() {
+  cat(geterrmessage(), file = stderr());
+  q("no", 1, F)
+}
+options(show.error.messages = F, error = err_foo)
 
 # Import required libraries
 suppressPackageStartupMessages({
-  library('getopt')
-  library('BioNet')
+  library("getopt")
+  library("BioNet")
 })
 
 # Take in trailing command line arguments
@@ -18,17 +19,16 @@
 
 # Get options using the spec as defined by the enclosed list
 # Read the options from the default: commandArgs(TRUE)
-option_specification <- matrix(c(
-  'input', 'i', 2, 'character',
-  'output', 'o', 2, 'character'
-), byrow=TRUE, ncol=4);
+option_specification <- matrix(c("input", "i", 2, "character",
+                                 "output", "o", 2, "character"
+                                ), byrow = TRUE, ncol = 4);
 
 # Parse options
 options <- getopt(option_specification);
 
 pvals <- read.table(options$input)
-bum <- fitBumModel(pvals,plot=FALSE)
+bum <- fitBumModel(pvals, plot = FALSE)
 mat <- c(bum$lambda, bum$a)
-#bumtablename <- paste(options$output,sep="\t")
-write.table(x=mat, file=options$output,quote=FALSE, row.names=FALSE, col.names=FALSE)
-message ("Parameters have been estimated successfully!")
+write.table(x = mat, file = options$output, quote = FALSE,
+            row.names = FALSE, col.names = FALSE)
+message("Parameters have been estimated successfully!")