<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>