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