# HG changeset patch
# User iuc
# Date 1430276218 14400
# Node ID 08452f5bf934edda36625c95d937c74e309dec66
# Parent 6daedea551df2381200552fb2a2803cae9fe0dbf
Uploaded
diff -r 6daedea551df -r 08452f5bf934 abyss-pe.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/abyss-pe.xml Tue Apr 28 22:56:58 2015 -0400
@@ -0,0 +1,63 @@
+
+ Assemble short paired reads
+
+ macros.xml
+
+
+
+ abyss-pe_wrapper.pl
+$k
+$n
+$outfile.extra_files_path
+$outfile
+$contigs_outfile
+$sam_outfile
+$coverage_histogram_outfile
+#for $i in $infiles
+${i.infile}
+#end for
+
+
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+
+**What it does**
+
+ABySS is a de novo, paired-end sequence assembler that is designed for short reads.
+
+**Input**
+
+The suffix of the read identifier for a pair of reads must be one of '1' and '2', or 'A' and 'B', or 'F' and 'R', or 'F3' and 'R3', or 'forward' and 'reverse'. The reads may be interleaved in the same file or found in different files; however, interleaved mates will use less memory.
+
+**Description**
+
+This tool performs the following commands:
+
+ABYSS - the single-end assembler
+AdjList - finds overlaps of length k-1 between contigs
+KAligner** - aligns reads to contigs
+ParseAligns** - finds pairs of reads in alignments
+DistanceEst** - estimates distances between contigs
+Overlap - find overlaps between blunt contigs
+SimpleGraph - finds paths between pairs of contigs
+MergePaths - merges consistent paths
+Consensus - for a colour-space assembly, convert the colour-space contigs to nucleotide contigs
+
+**Reference**
+
+http://www.bcgsc.ca/platform/bioinfo/software/abyss
+
+
diff -r 6daedea551df -r 08452f5bf934 abyss-pe_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/abyss-pe_wrapper.pl Tue Apr 28 22:56:58 2015 -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 () { print STDERR $_ }
+ close IN;
+ die("ABORTING\n");
+}
+
+# FILTER HISTOGRAM
+open (IN, "<$outdir/abyss.stderr") or die($!);
+open (OUT, ">$outfile") or die($!);
+while (my $line=) {
+ 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 () {
+ 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__
diff -r 6daedea551df -r 08452f5bf934 abyss.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/abyss.xml Tue Apr 28 22:56:58 2015 -0400
@@ -0,0 +1,34 @@
+
+ Assemble short unpaired reads
+
+ macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+ABySS is a de novo sequence assembler that is designed for short reads.
+
+.. image:: http://www.bcgsc.ca/platform/bioinfo/software/abyss/screenshot
+
+**Reference**
+
+http://www.bcgsc.ca/platform/bioinfo/software/abyss
+
+
diff -r 6daedea551df -r 08452f5bf934 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Apr 28 22:56:58 2015 -0400
@@ -0,0 +1,18 @@
+
+
+
+ abyss
+
+
+ ABYSS --version | head -n 1
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