diff qualitymetrics_wrapper.R @ 0:b4f5b5bc01dd draft

planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qualitymetrics_wrapper.R	Sat Aug 06 12:01:17 2016 -0400
@@ -0,0 +1,51 @@
+#!/usr/bin/Rscript --vanilla --slave --no-site-file
+
+################################################################################################
+# WRAPPER FOR QC_script.R (ANALYSES FOR QUALITY CONTROL)                                       #
+#                                                                                              #
+# Author: Melanie PETERA based on Marion LANDI's filters' wrapper                              #
+# User: Galaxy                                                                                 #
+# Original data: used with QC_script.R                                                         #
+# Starting date: 04-09-2014                                                                    #
+# V-1: Restriction of old filter wrapper to quality control (CV)                               #
+#                                                                                              #
+#                                                                                              #
+# Input files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt                      #
+# Output files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt                     #
+#                                                                                              #
+################################################################################################
+
+
+library(batch) #necessary for parseCommandArgs function
+args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
+
+source_local <- function(...){
+	argv <- commandArgs(trailingOnly = FALSE)
+	base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+	for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))}
+}
+#Import the different functions
+source_local("qualitymetrics_script.R", "easyrlibrary-lib/RcheckLibrary.R", "easyrlibrary-lib/miniTools.R")
+
+
+suppressMessages(library(ropls)) ## to be used in qualityMetricsF
+
+if(packageVersion("ropls") < "1.4.0")
+    stop("Please use 'ropls' versions of 1.4.0 and above")
+
+if(length(args) < 9){ stop("NOT enough arguments !!!") }
+
+args$Compa <- as.logical(args$Compa)
+args$poolAsPool1L <- as.logical(args$poolAsPool1L)
+
+QualityControl(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in,
+               args$CV, args$Compa, args$seuil, args$poolAsPool1L,
+               args$dataMatrix_out, args$sampleMetadata_out, args$variableMetadata_out, args$figure, args$information)
+
+#QualityControl(ion.file.in, meta.samp.file.in, meta.ion.file.in,
+#       CV, Compa, seuil,
+#       ion.file.out, meta.samp.file.out, meta.ion.file.out)
+
+#delete the parameters to avoid the passage to the next tool in .RData image
+rm(args)
+