--- /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>