--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abyss_toolsuite-92636934a189/abyss/abyss-pe_wrapper.pl	Mon Jun 11 14:48:15 2012 -0400
@@ -0,0 +1,90 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Copy;
+
+die("ERROR: Expected at least 8 arguments; got: @ARGV\n") unless @ARGV >= 8;
+
+# GET ARGS
+my $kmer_size=shift @ARGV;
+my $min_num_pairs=shift @ARGV;
+my $outdir=shift @ARGV;
+my $outfile=shift @ARGV;
+my $contigs_outfile=shift @ARGV;
+my $sam_outfile=shift @ARGV;
+my $hist_outfile=shift @ARGV;
+
+# ALL FILES GO IN THIS extra_files_path
+unless (-d $outdir) {
+    mkdir $outdir or die("Unable to make dir, $outdir\n");
+}
+chdir $outdir;
+
+# RUN COMMAND
+`abyss-pe k=$kmer_size n=$min_num_pairs in='@ARGV' name=abyss 2> $outdir/abyss.stderr > $outdir/abyss.stdout`;
+if ($? != 0) {
+    unless ( -s "$outdir/abyss-3.hist") { print STDERR "NO CONTIGS WERE PRODUCED!\n" }
+    open(IN, "<$outdir/abyss.stdout") or die($!);
+    while (<IN>) { print STDERR $_ }
+    close IN;
+    die("ABORTING\n");
+}
+
+# FILTER HISTOGRAM
+open (IN, "<$outdir/abyss.stderr") or die($!);
+open (OUT, ">$outfile") or die($!);
+while (my $line=<IN>) {
+    my @chars=split(//, $line);
+    my $filter=0;
+    foreach my $char (@chars) {
+        if (ord($char) >= 129) {
+            $filter=1;
+            last;
+        }
+    }
+    print OUT $line unless $filter;
+}
+close IN;
+close OUT;
+unlink("$outdir/abyss.stderr");
+
+# OUTPUT INFO LINE TEXT
+open(IN, "<$outdir/abyss.stdout") or die($!);
+while (<IN>) {
+    if (/^Assembled \d+ k\-mer in \d+ contigs/) {
+        print;
+        last;
+    }
+}
+close IN;
+
+# GALAXY DOESN'T WANT GZIPPED DATAFILES
+run("gunzip $outdir/abyss-3.sam.gz");
+
+# MOVE OUTFILES
+mv_outfile("$outdir/abyss-contigs.fa", $contigs_outfile);
+mv_outfile("$outdir/abyss-3.sam", $sam_outfile);
+mv_outfile("$outdir/coverage.hist", $hist_outfile);
+exit;
+
+sub run {
+    my $cmd=shift;
+    my $output=`$cmd 2>&1`;
+    if ($? != 0) {
+        print STDERR "ERROR RUNNING COMMAND: $cmd\n";
+        die($output);
+    }
+    return $output;
+}
+
+
+sub mv_outfile {
+    my ($src,$dest)=@_;
+    # if dest defined and src exist, then move outfiles to galaxy-specified location
+    if ( $dest ne 'None' and -f $src ) {
+        unlink($dest);
+        move($src,$dest);
+    }
+}
+__END__