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/tools/ilmn_pacbio/quake_pe.xml

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