diff bum.R @ 0:e41ec5af7472 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bum.R	Thu Aug 02 11:57:44 2018 -0400
@@ -0,0 +1,34 @@
+# Author: Cico Zhang
+# 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")
+
+# Import required libraries
+suppressPackageStartupMessages({
+  library('getopt')
+  library('BioNet')
+})
+
+# Take in trailing command line arguments
+args <- commandArgs(trailingOnly = TRUE)
+
+# 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);
+
+# Parse options
+options <- getopt(option_specification);
+
+pvals <- read.table(options$input)
+bum <- fitBumModel(pvals,plot=FALSE)
+mat <- c(bum$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!")