Mercurial > repos > xuebing > sharplabtool
view tools/ilmn_pacbio/quake.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -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>