<tool id="sopra_wpc" name="SOPRA with prebuilt contigs" version="0.1">
  <description>for Illumina libraries</description>
  <requirements>
    <requirement type="package" version="1.4.6">sopra</requirement>
    <requirement type="package" version="1.0.0">bowtie</requirement>
  </requirements>
  <command interpreter="python">
    sopra_wpc.py -p \${GALAXY_SLOTS:-1}
    #for $cr in $contigs_repeat
      --contigs ${cr.contigs_file}
    #end for
    #for $mr in $mate_repeat
      --mate ${mr.mate_file}
      -d ${mr.insert_size}
    #end for
    -v $max_mismatches -c $c_option -w $w_option -L $L_option --h_option $h_option --scaffolds $scaffolds_file --logfile $logfile
  </command>
  <inputs>
    <repeat name="contigs_repeat" title="Contigs file" min="1">
      <param name="contigs_file" type="data" format="fasta" label="Contigs" help="FASTA format" />
    </repeat>
    <repeat name="mate_repeat" title="Paired-end Illumina library" min="1">
      <param name="mate_file" type="data" format="fasta" label="Paired-end Illumina library" help="FASTA format" />
      <param name="insert_size" type="integer" value="" label="Insert size" help="Insert size for the library (-d)" />
    </repeat>
    <param name="max_mismatches" type="integer" min="0" max="3" value="0" label="Maximum number of mismatches when aligning reads on contigs with Bowtie (-v)" help="May be 0, 1, 2, or 3" />
    <param name="c_option" type="integer" value="5" label="If the number of times a read and its reverse complement appear in the library is equal to or more than this value, the pairing information from that read will be disregarded (-c)" />
    <param name="w_option" type="integer" value="4" label="Minimum number of links between two contigs (-w)" />
    <param name="L_option" type="integer" value="150" label="Minimum length of contigs to be used in scaffold assembly (-L)" />
    <param name="h_option" type="float" value="2.2" label="h value (-h)" help="High coverage contigs (above mean_coverage + h x std_coverage) are not considered in the scaffold assembly mainly to exclude reads from repetitive regions" />
  </inputs>
  <outputs>
    <data format="fasta" name="scaffolds_file" label="${tool.name} on ${on_string}: scaffolds_sopra.fasta"/>
    <data format="txt" name="logfile" label="${tool.name} on ${on_string}: log"/>
  </outputs>
  <help>
**What it does**

SOPRA is a scaffold assembly tool for paired-end/mate pair data generated by high-throughput sequencing technologies, e.g. Illumina and SOLiD platforms. This wrapper currently supports only Illumina paired-end data.

Bowtie is used to align the reads to the contigs.

The input paired-end FASTA file can be obtained with:
FR reads -> *FASTQ interlacer on paired end reads* followed by *FASTQ to FASTA* converter
RF reads -> *Reverse-Complement*, *FASTQ interlacer on paired end reads* followed by *FASTQ to FASTA* converter

.. class:: infomark

**TIP:** Try trimming the end of short reads before feeding it to the assembler to remove the error prone bases (e.g. last 10 to 20 bps) and check if it improves the assembly.

-----

**License and citation**

This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.

.. _CRS4 Srl.: http://www.crs4.it/
.. _MIT license: http://opensource.org/licenses/MIT

If you use this tool in Galaxy, please cite |Cuccuru2013|_.

.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
.. _Cuccuru2013: http://orione.crs4.it/

This tool uses `SOPRA`_, which is licensed separately. Please cite |Dayarian2010|_.

.. _SOPRA: http://www.physics.rutgers.edu/~anirvans/SOPRA/
.. |Dayarian2010| replace:: Dayarian, A., Michael, T. P., Sengupta, A. M. (2010) SOPRA: Scaffolding algorithm for paired reads via statistical optimization. *BMC Bioinformatics* 11, 345
.. _Dayarian2010: http://www.biomedcentral.com/1471-2105/11/345/
  </help>
</tool>