--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ilmn_pacbio/quake_pe.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,53 @@
+<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>