--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mosaics_wrapper.pl	Thu Jan 10 15:57:13 2013 -0500
@@ -0,0 +1,99 @@
+# Wrapper for MOSAiCS
+# Written by Dongjun Chung, Jan. 15, 2013
+
+#!/usr/bin/env perl;
+use warnings;
+use strict;
+use File::Temp qw/tempfile/;
+use File::Temp qw/tempdir/;
+use File::Basename;
+
+# parse command arguments
+# inactive arguments: useChrfile, chrfile, excludeChr
+# meaningless argument: analysisType (for later use)
+
+die "Usage: perl mosaics_wrapper.pl [chip_path] [chip_file_format] [control_path] [control_file_format] [peak_path] [peak_file_format] [analysis_type] [report_summary_path] [report_gof_path] [report_exploratory_path] [PET?] [chromosome-wise?] [fdr_level] [frag_len] [bin_size] [capping] [signal_model] [bg_est_method] [d] [maxgap] [minsize] [thres] [parallel] [n_core]" unless @ARGV == 24;
+
+my ( $chip_path, $chip_file_format, $control_path, $control_file_format, $peak_path, $peak_file_format, $analysis_type, $report_summary_path, $report_gof_path, $report_exploratory_path, $pet, $by_chr, $fdr_level, $frag_len, $bin_size, $capping, $signal_model, $bg_est_method, $d, $maxgap, $minsize, $thres, $parallel, $n_core ) = @ARGV;
+
+# parse options: analysis type
+
+if ( $analysis_type ne "IO" ) {
+	print "Only 'IO' is supported for analysis type!\n";
+	exit 1;	
+}
+
+
+# parse options: report summary
+
+my $report_summary = "FALSE";
+if ( $report_summary_path ne "None" ) {
+	$report_summary = "TRUE";
+}
+
+# parse options: report GOF
+
+my $report_gof = "FALSE";
+if ( $report_gof_path ne "None" ) {
+	$report_gof = "TRUE";
+}
+
+# parse options: report exploratory analysis
+
+my $report_exploratory = "FALSE";
+if ( $report_exploratory_path ne "None" ) {
+	$report_exploratory = "TRUE";
+}
+
+# write a R scrip to run
+
+my $tempdir_bin = tempdir();
+
+my $cmd = qq|
+	suppressPackageStartupMessages(library(mosaics))
+	try( suppressPackageStartupMessages(library(parallel)), silent=TRUE )
+	
+	mosaicsRunAll( 
+		chipFile="$chip_path", 
+		chipFileFormat="$chip_file_format", 
+		controlFile="$control_path", 
+		controlFileFormat="$control_file_format",
+		binfileDir="$tempdir_bin",
+		peakFile="$peak_path", 
+		peakFileFormat="$peak_file_format",
+		reportSummary=$report_summary, 
+		summaryFile="$report_summary_path", 
+		reportExploratory=$report_exploratory,
+		exploratoryFile="$report_exploratory_path", 
+		reportGOF=$report_gof,
+		gofFile="$report_gof_path", 
+		PET=$pet, 
+		byChr=$by_chr, 
+		useChrfile=FALSE, 
+		chrfile=NULL, 
+		excludeChr=NULL, 
+		FDR=$fdr_level, 
+		fragLen=$frag_len, 
+		binSize=$bin_size, 
+		capping=$capping, 
+		bgEst="$bg_est_method",
+		d=$d, 
+		signalModel="$signal_model", 
+		maxgap=$maxgap, 
+		minsize=$minsize, 
+		thres=$thres, 
+		parallel=$parallel,
+		nCore=$n_core )
+	
+	q()
+	|;
+
+# run R
+
+open( FT, "| R --slave --vanilla >& /dev/null" ) or die "Couldn't call R!\n";
+print FT $cmd, "\n";
+close FT or die "Couldn't finish R!\n";
+
+exit;
+
+