<tool id='duk' name='duk' version='1.0.3' description='Filter nextgen reads'>
<command>duk
-n $passfile
#if $badreads.select == 'yes':
-m $failfile
#end if
-k $kmer
-s $step
-c $cutoff
$source.file
$input 
</command>
<inputs>
    <param name="input" type="data" format="fastq,fastqillumina,fastqsanger" label="Fastq file of reads"/>
    <conditional name='source'>
        <param name='select' type='select' label='[-d] Target database'>
            <option value='adapterdb'>Precompiled Adapter Db</option>
            <option value='contamdb'>Precompiled Contaminants Db</option>
            <option value='user'>History file</option>
        </param>
        <when value='adapterdb'>
            <param name="file" type="select" label="Precompiled adapter database">
                <options from_file="adapterdb.loc">
                  <column name="name" index="1"/>
                  <column name="value" index="2"/>
                </options>
            </param>
        </when>
        <when value='contamdb'>
            <param name="file" type="select" label="Precompiled contaminants database">
                <options from_file="contamdb.loc">
                  <column name="name" index="1"/>
                  <column name="value" index="2"/>
                </options>
            </param>
        </when>
        <when value='user'>
            <param name='file' type='data' format='fasta' label='Fasta file'/>
        </when>
    </conditional>
    <param name='kmer' type='integer' value='16' label='[-kmer] the k mer size' />
    <param name='step' type='integer' value='5' label='[-step] the step size' />
    <param name='cutoff' type='integer' value='1' label='[-cutoff] the cut off threshold for contaminated reads' />
    <conditional name='badreads'>
        <param name='select' type='select' display='radio' label='Save filtered reads?'>
            <option value='yes'>Yes, save to file</option>
            <option value='no'>No, discard</option>
        </param>
        <when value='yes'>
        </when>
        <when value='no'>
        </when>
    </conditional>

</inputs>
<outputs>
    <data name='passfile' format='input' />
    <data name='failfile' format='input' label='Failed reads'>
        <filter>badreads["select"] == "yes"</filter>
    </data>
</outputs>
<help>
**What It Does**

Filters reads containing undesired sequences, such as library artifacts or ribosomal sequences.

Decrease the step size to increase the sensitivity.

A kmer setting 16 means that any contaminant sequence less than 16 bases would slip through.

Lastly, contaminants with 'N' bases (no call) are more likely to be missed.

**Author**

Mingkun Li (MLi@LBL.gov)
</help>
</tool>