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author edward-kirton
date Thu, 14 Jul 2011 22:25:21 -0400
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-1:000000000000 0:6e61b7ddb5f9
1 <tool id='duk' name='duk' version='1.0.3' description='Filter nextgen reads'>
2 <command>duk
3 -n $passfile
4 #if $badreads.select == 'yes':
5 -m $failfile
6 #end if
7 -k $kmer
8 -s $step
9 -c $cutoff
10 $source.file
11 $input
12 </command>
13 <inputs>
14 <param name="input" type="data" format="fastq,fastqillumina,fastqsanger" label="Fastq file of reads"/>
15 <conditional name='source'>
16 <param name='select' type='select' label='[-d] Target database'>
17 <option value='adapterdb'>Precompiled Adapter Db</option>
18 <option value='contamdb'>Precompiled Contaminants Db</option>
19 <option value='user'>History file</option>
20 </param>
21 <when value='adapterdb'>
22 <param name="file" type="select" label="Precompiled adapter database">
23 <options from_file="adapterdb.loc">
24 <column name="name" index="1"/>
25 <column name="value" index="2"/>
26 </options>
27 </param>
28 </when>
29 <when value='contamdb'>
30 <param name="file" type="select" label="Precompiled contaminants database">
31 <options from_file="contamdb.loc">
32 <column name="name" index="1"/>
33 <column name="value" index="2"/>
34 </options>
35 </param>
36 </when>
37 <when value='user'>
38 <param name='file' type='data' format='fasta' label='Fasta file'/>
39 </when>
40 </conditional>
41 <param name='kmer' type='integer' value='16' label='[-kmer] the k mer size' />
42 <param name='step' type='integer' value='5' label='[-step] the step size' />
43 <param name='cutoff' type='integer' value='1' label='[-cutoff] the cut off threshold for contaminated reads' />
44 <conditional name='badreads'>
45 <param name='select' type='select' display='radio' label='Save filtered reads?'>
46 <option value='yes'>Yes, save to file</option>
47 <option value='no'>No, discard</option>
48 </param>
49 <when value='yes'>
50 </when>
51 <when value='no'>
52 </when>
53 </conditional>
54
55 </inputs>
56 <outputs>
57 <data name='passfile' format='input' />
58 <data name='failfile' format='input' label='Failed reads'>
59 <filter>badreads["select"] == "yes"</filter>
60 </data>
61 </outputs>
62 <help>
63 **What It Does**
64
65 Filters reads containing undesired sequences, such as library artifacts or ribosomal sequences.
66
67 Decrease the step size to increase the sensitivity.
68
69 A kmer setting 16 means that any contaminant sequence less than 16 bases would slip through.
70
71 Lastly, contaminants with 'N' bases (no call) are more likely to be missed.
72
73 **Author**
74
75 Mingkun Li (MLi@LBL.gov)
76 </help>
77 </tool>