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1 <tool id="quake_pe" name="Quake PE" version="1.0.0">
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2 <description>Quality-aware error correction for paired-end reads</description>
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3 <command interpreter="python">
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4 quake_wrapper.py --default_cutoff=$cutoff --headers -k $k -f $fofnfile -p 12 --output=$output1,$output2
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5 </command>
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6 <inputs>
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7 <param name="input1" format="fastq" type="data" label="FASTQ file for forward reads" />
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8 <param name="input2" format="fastq" type="data" label="FASTQ file for reverse reads" />
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9 <param name="k" type="integer" value="16" label="Size of k-mers to correct" />
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10 <param name="cutoff" type="integer" value="0" label="Default coverage cutoff if estimation fails"/>
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11 </inputs>
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12 <configfiles>
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13 <configfile name="fofnfile">${input1.file_name} ${input2.file_name}
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14 </configfile>
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15 </configfiles>
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16 <outputs>
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17 <data format="fastq" name="output1" label="Error-corrected forward reads from ${on_string}" />
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18 <data format="fastq" name="output2" label="Error-corrected reverse reads from ${on_string}" />
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19 </outputs>
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20 <help>
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21
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22 **What it does**
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23
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24 Applies the Quake_ algorithm for quality-aware correction of
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25 substitution error in short reads. This form of the tool is customized
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26 for correcting paired-end reads.
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27
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28 Kelley DR, Schatz MC, Salzberg SL.
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29 "Quake: quality-aware detection and correction of sequencing errors."
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30 *Genome Biol.* 2010;11(11):R116.
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31
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32 .. _Quake: http://www.cbcb.umd.edu/software/quake
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33
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34 **Parameter list**
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35
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36 K-mer size
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37 k-mer size for detecting spurious k-mers versus true k-mers from
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38 the genome. Recommendations for choosing a value of k can be found
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39 here_.
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40
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41 Default coverage cutoff
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42 If the appropriate coverage cutoff can not be found then Quake can be
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43 forced to proceed anyways with the supplied cutoff. In this case,
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44 the optimal cutoff can be estimated by examining
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45 the k-mer coverage histogram by eye.
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46
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47 .. _here: http://www.cbcb.umd.edu/software/quake/faq.html
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48
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49 **Output**
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50
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51 A FASTQ file of corrected and trimmed reads.
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52 </help>
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53 </tool>
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