# HG changeset patch
# User g2cmnty@test-web1.g2.bx.psu.edu
# Date 1309271349 14400
# Node ID a188de29f06e7f6a7e43352f2b29714a204926f7
# Parent  6ad594db014300c75defdfb4934e5513a37178f2
Uploaded

diff -r 6ad594db0143 -r a188de29f06e abyss/abyss-pe.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abyss/abyss-pe.xml	Tue Jun 28 10:29:09 2011 -0400
@@ -0,0 +1,58 @@
+<tool id="abyss-pe" name="Abyss Paired-End" version="1.0.0">
+<description>Assemble short paired reads</description>
+<command interpreter='perl'>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
+</command>
+
+<inputs>
+    <repeat name="infiles" title="Paired Reads Files">
+        <param name="infile" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired read sequences"/>
+    </repeat>
+    <param name="k" type="integer" value="41" label="[-k] K-mer size" help="Try multiple sizes, starting around 2/3 read length" />
+    <param name="n" type="integer" value="10" label="[-n] Min. num. pairs for scaffolding" help="Requirement for joining contigs into a scaffold" />
+</inputs>
+
+<outputs>
+    <data name="outfile" format="txt" />
+    <data name="contigs_outfile" format="fasta" label="Contigs" />
+    <data name="sam_outfile" format="sam" label="Read aligments (Sam)" />
+    <data name="coverage_histogram_outfile" format="txt" label="Coverage histogram" />
+</outputs>
+
+<help>
+**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
+</help>
+</tool>
diff -r 6ad594db0143 -r a188de29f06e abyss/abyss-pe_wrapper.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abyss/abyss-pe_wrapper.pl	Tue Jun 28 10:29:09 2011 -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__
diff -r 6ad594db0143 -r a188de29f06e abyss/abyss.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abyss/abyss.xml	Tue Jun 28 10:29:09 2011 -0400
@@ -0,0 +1,25 @@
+<tool id="abyss" name="Abyss" version="1.0.0">
+<description>Assemble short unpaired reads</description>
+<command interpreter='bash'>abyss_wrapper.sh $k $infile $outfile</command>
+
+<inputs>
+    <param name="infile" type="data" format="fasta|fastq" label="Unpaired read sequences" />
+    <param name="k" type="integer" value="41" label="K-mer size" help="Try multiple sizes, starting around 2/3 read length" />
+</inputs>
+
+<outputs>
+    <data name="outfile" format="fasta" />
+</outputs>
+
+<help>
+**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
+</help>
+</tool>
diff -r 6ad594db0143 -r a188de29f06e abyss/abyss_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abyss/abyss_wrapper.sh	Tue Jun 28 10:29:09 2011 -0400
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+if [ $# -ne 3 ]
+then
+    echo "ERROR: Expected exactly 3 arguments; got: $*" 1>&2
+    exit 1
+fi
+
+CMD=`ABYSS -k$1 $2 -o $3 2>&1`
+if [ $? -ne 0 ]
+then
+{
+    echo "COMMAND FAILURE: $CMD" 1>&2
+    exit $?
+}
+fi
diff -r 6ad594db0143 -r a188de29f06e abyss/suite_config.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abyss/suite_config.xml	Tue Jun 28 10:29:09 2011 -0400
@@ -0,0 +1,9 @@
+<suite id='abyss_toolsuite' name='Suite of Abyss assembler tools' version="1.0.0">
+	<description>This suite contains Abyss and Abyss-PE config files and wrappers for Galaxy</description>
+	<tool id="abyss" name="Abyss" version="1.0.0">
+		<description>Abyss (single-end) assembler</description>
+	</tool>
+	<tool id="abyss-pe" name="Abyss Paired-End" version="1.0.0">
+		<description>Abyss-PE (paired-end) assembler</description>
+	</tool>
+</suite>