diff summary_statistics_galaxy.R @ 0:46ddb0591d8b draft default tip

planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/summary_statistics_galaxy.R	Thu Jan 18 07:44:37 2018 -0500
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+###########################################################################
+#            Quality controls and descriptive analysis plots              #
+###########################################################################
+# Authors: Melanie Petera                                                 #
+###########################################################################
+# Description : This script allows various displays of data for quality   #
+#      control and descriptive analysis. The input data is a matrix of    #
+#      quantitative variables, and it returns chosen plots in png format  #
+#      and a table with chosen statistics.                                #
+###########################################################################
+# Specific R packages:                                                    #
+#      - edgeR (needed for MA plots)                                      #
+###########################################################################
+# Version 1 (06-06-2014): display boxplot, histogram, density plot,       #
+#      MA plot, pairs plot, and return a table of chosen statistics       #
+#      (quantiles, mean, variance, standard error of the mean)            #
+###########################################################################
+
+
+##------------------------------
+## Libraries laoding
+##------------------------------
+# For parseCommandArgs function
+library(batch) 
+
+# R script call
+source_local <- function(fname)
+{
+	argv <- commandArgs(trailingOnly = FALSE)
+	base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+	source(paste(base_dir, fname, sep="/"))
+}
+
+#Import the different functions used for Summary_Statistics
+source_local("summary_statistics.R")
+
+##------------------------------
+## Lecture parametres
+##------------------------------
+argLs <- parseCommandArgs(evaluate=FALSE)
+
+desc_fct(file.in=argLs[["file_in"]],
+nacode=argLs[["NA_code"]],
+table_file=argLs[["table_file"]],
+graph_file=argLs[["graph_file"]],
+stat=argLs[["stat"]],
+chosen.stat=argLs[["stat_chosen"]],
+ploting=argLs[["ploting"]],
+chosen.plot=argLs[["plot_chosen"]],
+log_file=argLs[["log_file"]])
+
+