--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/roche454/runMapping_cDNA_wrapper.pl	Tue Jun 07 17:50:32 2011 -0400
@@ -0,0 +1,96 @@
+#!/usr/bin/env/perl
+
+use warnings;
+use strict;
+use File::Copy;
+
+# EXPECT 21 FILE HANDLES, SOME OF WHICH MAY BE 'None'
+my $outdir=shift @ARGV;
+my $alignment_info=shift @ARGV;
+my $all_contigs_fasta=shift @ARGV;
+my $all_contigs_qual=shift @ARGV;
+my $all_diffs=shift @ARGV
+my $all_struct_vars=shift @ARGV
+my $hc_diff=shift @ARGV
+my $hc_struct_vars=shift @ARGV
+my $mapping_qc=shift @ARGV
+my $newbler_metrics=shift @ARGV;
+my $pair_align=shift @ARGV;
+my $read_status=shift @ARGV;
+my $ref_status=shift @ARGV;
+my $tag_pair_align=shift @ARGV;
+my $trim_status=shift @ARGV;
+my $trimmed_reads_fasta=shift @ARGV;
+my $trimmed_reads_qual=shift @ARGV;
+my $contigs_ace=shift @ARGV;
+my $gene_status=shift @ARGV;
+my $isotigs_ace=shift @ARGV;
+my $isotigs_fasta=shift @ARGV;
+my $isotigs_qual=shift @ARGV;
+my $isotigs_agp=shift @ARGV;
+my $isotigs_layout=shift @ARGV;
+ 
+# REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED
+
+my @cmd=removeUnusedOptions(@ARGV);
+
+# RUN COMMAND
+# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
+my $stderr;
+eval { $stderr=`@cmd 2>&1`; };
+if ( $@ ) {
+    print STDERR "Newbler ERROR: $stderr\n";
+    `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
+    die($@);
+}
+
+get_outfile("$outdir/454AlignmentInfo.tsv", $alignment_info);
+get_outfile("$outdir/454AllContigs.fna", $all_contigs_fasta);
+get_outfile("$outdir/454AllContigs.qual", $all_contigs_qual);
+get_outfile("$outdir/454AllDiffs.txt", $all_diffs);
+get_outfile("$outdir/454AllStructVars.txt", $all_struct_vars);
+get_outfile("$outdir/454HCDiff.txt", $hc_diff);
+get_outfile("$outdir/454HCStructVars.txt", $hc_struct_vars);
+get_outfile("$outdir/454MappingQC.xls", $mapping_qc);
+get_outfile("$outdir/454NewblerMetrics.txt", $newbler_metrics);
+get_outfile("$outdir/454PairAlign.txt", $pair_align);
+get_outfile("$outdir/454ReadStatus.txt", $read_status);
+get_outfile("$outdir/454RefStatus.txt", $ref_status);
+get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
+get_outfile("$outdir/454TrimStatus.txt", $trim_status);
+get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
+get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
+get_outfile("$outdir/454Contigs.ace", $contigs_ace);
+get_outfile("$outdir/454GeneStatus.txt", $gene_status);
+get_outfile("$outdir/454Isotigs.ace", $isotigs_ace);
+get_outfile("$outdir/454Isotigs.fna", $isotigs_fasta);
+get_outfile("$outdir/454Isotigs.qual", $isotigs_qual);
+get_outfile("$outdir/454Isotigs.txt", $isotigs_agp);
+get_outfile("$outdir/454IsotigsLayout.txt", $isotigs_layout);
+exit;
+
+# EVERY 'None' ARG AND IT'S PRECEEDING OPTION TAG ARE DISCARDED
+sub removeUnusedOptions {
+    my @cmd=();
+    my $prev;
+    foreach (@_) {
+        unless ($_ eq 'None') {
+            push @cmd, $prev if defined($prev);
+            $prev=$_;
+        } else {
+            $prev=undef;
+        }
+    }
+    push @cmd, $prev if defined($prev);
+    return @cmd;
+}
+
+sub get_outfile {
+    my ($src, $dest)=@_;
+    # make sure dest defined and src exist; skip if dest is 'None'
+    if ( $dest and $dest ne 'None' and $src and -f $src ) {
+        move($src,$dest);
+    }
+}
+
+__END__