<tool id="quake_pe" name="Quake PE" version="1.0.0">
  <description>Quality-aware error correction for paired-end reads</description>
  <command interpreter="python">
    quake_wrapper.py --default_cutoff=$cutoff --headers -k $k -f $fofnfile -p 12 --output=$output1,$output2
  </command>
  <inputs>
    <param name="input1" format="fastq" type="data" label="FASTQ file for forward reads" />
    <param name="input2" format="fastq" type="data" label="FASTQ file for reverse reads" />
    <param name="k" type="integer" value="16" label="Size of k-mers to correct" />
    <param name="cutoff" type="integer" value="0" label="Default coverage cutoff if estimation fails"/>
  </inputs>
  <configfiles>
    <configfile name="fofnfile">${input1.file_name} ${input2.file_name}
    </configfile>
  </configfiles>
  <outputs>
    <data format="fastq" name="output1" label="Error-corrected forward reads from ${on_string}" />
    <data format="fastq" name="output2" label="Error-corrected reverse reads from ${on_string}" />
  </outputs>
  <help>

**What it does**

Applies the Quake_ algorithm for quality-aware correction of
substitution error in short reads.  This form of the tool is customized
for correcting paired-end reads.

Kelley DR, Schatz MC, Salzberg SL.
"Quake: quality-aware detection and correction of sequencing errors."
*Genome Biol.* 2010;11(11):R116.

.. _Quake: http://www.cbcb.umd.edu/software/quake

**Parameter list**

K-mer size
    k-mer size for detecting spurious k-mers versus true k-mers from
    the genome.  Recommendations for choosing a value of k can be found
    here_.

Default coverage cutoff
    If the appropriate coverage cutoff can not be found then Quake can be
    forced to proceed anyways with the supplied cutoff.  In this case, 
    the optimal cutoff can be estimated by examining
    the k-mer coverage histogram by eye.

.. _here: http://www.cbcb.umd.edu/software/quake/faq.html

**Output**

A FASTQ file of corrected and trimmed reads.
  </help>
</tool>