--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/duk.xml	Thu Jul 14 22:25:21 2011 -0400
@@ -0,0 +1,77 @@
+<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>