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1 <tool id="quake" name="Quake" version="1.0.0">
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2 <description>Quality-aware error correction</description>
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3 <command interpreter="python">
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4 quake_wrapper.py --default_cutoff=10 --headers -k $k -f $fofnfile -p 12 > $output1
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5 </command>
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6 <inputs>
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7 <param name="input1" format="fastq" type="data" label="Select FASTQ file to correct" />
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8 <param name="k" type="integer" value="16" label="Size of k-mers to correct" />
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9 </inputs>
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10 <configfiles>
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11 <configfile name="fofnfile">
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12 ${input1.file_name}
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13 </configfile>
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14 </configfiles>
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15 <outputs>
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16 <data format="fastq" name="output1" label="Error-corrected reads from ${on_string}" />
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17 </outputs>
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18 <help>
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19
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20 **What it does**
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21
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22 Applies the Quake_ algorithm for quality-aware correction of
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23 substitution error in short reads.
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24
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25 Kelley DR, Schatz MC, Salzberg SL.
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26 "Quake: quality-aware detection and correction of sequencing errors."
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27 *Genome Biol.* 2010;11(11):R116.
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28
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29 .. _Quake: http://www.cbcb.umd.edu/software/quake
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30
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31 **Parameter list**
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32
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33 k
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34 k-mer size for detecting spurious k-mers versus true k-mers from
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35 the genome. Recommendations for choosing a value of k can be found
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36 here_.
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37
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38 .. _here: http://www.cbcb.umd.edu/software/quake/faq.html
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39
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40 **Output**
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41
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42 A FASTQ file of corrected and trimmed reads.
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43 </help>
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44 </tool>
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