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author msjeon
date Mon, 11 Jun 2012 15:53:09 -0400
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1 <tool id="abyss-pe" name="Abyss Paired-End" version="1.0.0">
2 <description>Assemble short paired reads</description>
3 <command interpreter='perl'>abyss-pe_wrapper.pl
4 $k
5 $n
6 $outfile.extra_files_path
7 $outfile
8 $contigs_outfile
9 $sam_outfile
10 $coverage_histogram_outfile
11 #for $i in $infiles
12 ${i.infile}
13 #end for
14 </command>
15
16 <inputs>
17 <repeat name="infiles" title="Paired Reads Files">
18 <param name="infile" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired read sequences"/>
19 </repeat>
20 <param name="k" type="integer" value="41" label="[-k] K-mer size" help="Try multiple sizes, starting around 2/3 read length" />
21 <param name="n" type="integer" value="10" label="[-n] Min. num. pairs for scaffolding" help="Requirement for joining contigs into a scaffold" />
22 </inputs>
23
24 <outputs>
25 <data name="outfile" format="txt" />
26 <data name="contigs_outfile" format="fasta" label="Contigs" />
27 <data name="sam_outfile" format="sam" label="Read aligments (Sam)" />
28 <data name="coverage_histogram_outfile" format="txt" label="Coverage histogram" />
29 </outputs>
30
31 <help>
32 **What it does**
33
34 ABySS is a de novo, paired-end sequence assembler that is designed for short reads.
35
36 **Input**
37
38 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.
39
40 **Description**
41
42 This tool performs the following commands:
43
44 ABYSS - the single-end assembler
45 AdjList - finds overlaps of length k-1 between contigs
46 KAligner** - aligns reads to contigs
47 ParseAligns** - finds pairs of reads in alignments
48 DistanceEst** - estimates distances between contigs
49 Overlap - find overlaps between blunt contigs
50 SimpleGraph - finds paths between pairs of contigs
51 MergePaths - merges consistent paths
52 Consensus - for a colour-space assembly, convert the colour-space contigs to nucleotide contigs
53
54 **Reference**
55
56 http://www.bcgsc.ca/platform/bioinfo/software/abyss
57 </help>
58 </tool>