# HG changeset patch
# User iuc
# Date 1429066021 14400
# Node ID 1d0f1274d99904dc19737c2450a0c3388bfe40b5
Uploaded
diff -r 000000000000 -r 1d0f1274d999 abyss-pe.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/abyss-pe.xml Tue Apr 14 22:47:01 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 000000000000 -r 1d0f1274d999 abyss-pe_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/abyss-pe_wrapper.pl Tue Apr 14 22:47:01 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 000000000000 -r 1d0f1274d999 abyss.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/abyss.xml Tue Apr 14 22:47:01 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 000000000000 -r 1d0f1274d999 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Apr 14 22:47:01 2015 -0400
@@ -0,0 +1,18 @@
+
+
+
+ abyss
+
+
+ ABYSS --version | head -n 1
+
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+