diff tools/ilmn_pacbio/quake.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ilmn_pacbio/quake.xml	Fri Mar 09 19:37:19 2012 -0500
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+<tool id="quake" name="Quake" version="1.0.0">
+  <description>Quality-aware error correction</description>
+  <command interpreter="python">
+    quake_wrapper.py --default_cutoff=10 --headers -k $k -f $fofnfile -p 12 > $output1
+  </command>
+  <inputs>
+    <param name="input1" format="fastq" type="data" label="Select FASTQ file to correct" />
+    <param name="k" type="integer" value="16" label="Size of k-mers to correct" />
+  </inputs>
+  <configfiles>
+    <configfile name="fofnfile">
+${input1.file_name}
+    </configfile>
+  </configfiles>
+  <outputs>
+    <data format="fastq" name="output1" label="Error-corrected reads from ${on_string}" />
+  </outputs>
+  <help>
+
+**What it does**
+
+Applies the Quake_ algorithm for quality-aware correction of
+substitution error in short 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
+    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_.
+
+.. _here: http://www.cbcb.umd.edu/software/quake/faq.html
+
+**Output**
+
+A FASTQ file of corrected and trimmed reads.
+  </help>
+</tool>