<tool id="phrap" name="Phrap" version="1.0.0">
<description>Assemble long reads/short contigs</description>
<command interpreter='bash'>phrap_wrapper.sh $label $fasta_infile $qual_infile $fasta_outfile $qual_outfile $singlets_outfile $fasta_outfile.extra_files_path</command>

<inputs>
    <param name="label" type="text" value="seqs" label="Label for naming contig sequences (e.g. library or sample name)" help="Contigs will be named LABEL.Contig1, ..." />
    <param name="fasta_infile" type="data" format="fasta" label="Long reads or contig sequences" />
    <param name="qual_infile" type="data" format="qual" optional='True' label="Optional sequence quality scores (Phred-scaled)" />
</inputs>

<outputs>
    <data name="fasta_outfile" format="fasta" />
    <data name="qual_outfile" format="qual" label="Contig quality scores" />
    <data name="singlets_outfile" format="fasta" label="Singlets Fasta" />
</outputs>

<help>
**What it does**

phrap ("phragment assembly program", or "phil's revised assembly
program"; a homonym of "frappe" = French for "swat") -- a
program for assembling shotgun DNA sequence data.  Key features:
allows use of entire read (not just trimmed high quality part); uses a
combination of user-supplied and internally computed data quality
information to improve accuracy of assembly in the presence of
repeats; constructs contig sequence as a mosaic of the highest quality
parts of reads (rather than a consensus); provides extensive information
about assembly (including quality values for contig sequence) to
assist trouble-shooting; able to handle very large datasets.

**Notes**

phrap is great for assembling Sanger shotgun reads but should not be used for next-generation data (e.g. Illumina, Solid, 454, etc.).
However phrap is useful for combining short-read assemblies from Velvet or Abyss (i.e. results from using multiple k-mer parameters). 
When used for this purpose, you should filter out short sequences first (e.g. less than 200-1000bp, depending on number of contigs).

**Reference**

http://www.phrap.org/phredphrap/phrap.html
</help>
</tool>