--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lighter.xml	Sat Jun 04 12:38:34 2016 -0400
@@ -0,0 +1,92 @@
+<tool id="lighter" name="lighter" version="1.0" profile="16.04">
+    <description>can correct the reads containing sequence errors</description>
+    <requirements>
+        <requirement type="package" version="1.1.1">lighter</requirement>
+    </requirements>
+    <command><![CDATA[
+       lighter
+           #for $file in $r:
+               -r $file
+           #end for
+           #if str($kmer.k_select) == "smallk":
+               -k $kmer.k_parameter_string
+           #elif str($kmer.k_select) == "bigK":
+               -K $kmer.K_parameter_string 
+           #end if
+           -od ./
+           -t \${GALAXY_SLOTS:-4}
+           #if $maxcor:
+               -maxcor $maxcor
+           #end if
+           $trim
+           $discard
+           $noQual
+           #if $newQual:
+               -newQual '$newQual'
+           #end if
+           $stable
+            > $outfile
+    ]]>
+    </command>
+    <inputs>
+        <param argument="-r" multiple="True" type="data" label="Input file"/>
+        <conditional name="kmer">
+            <param name="k_select" type="select" label="Do you want k or K?">
+                <option value="smallk">small k</option>
+                <option value="bigK">big K</option>
+            </param>
+            <when value="smallk">
+                <param name="k_parameter_string" size="30" type="text" value="13 20 0.2" label="type in 3 parameters"
+                    help="(—k kmer_length genome_size alpha)" />
+            </when>
+            <when value="bigK">
+                <param name="K_parameter_string" size="30" type="text" value="13 20" label="type in 2 parameters"
+                    help="(—K kmer_length genome_size)" />
+            </when>
+        </conditional>
+        <param argument="-maxcor" type="integer" value="4" optional="True" 
+            label="Maximum number of correction for within a kmer length window" help=""/>
+        <param argument="-trim" type="boolean" truevalue="-trim" falsevalue="" checked="False" 
+            label="Whether or not to allow trimming"/>
+        <param argument="-discard" type="boolean" truevalue="-discard" falsevalue="" checked="False" 
+            label="Whether or not to discard unfixable reads. Will lose paired-end matching when discarding"/>
+        <param argument="-noQual" type="boolean" truevalue="-noQual" falsevalue="" checked="False" 
+            label="Whether or not to ignore the quality socre"/>
+        <param argument="-newQual" size="30" type="text" value="" optional="True" 
+            label="Quality for the bases corrected to the specified score" help="" />
+        <param argument="-stable" type="boolean" truevalue="-stable" falsevalue="" checked="False"
+            label="Sequentialize the sampling stage, output the same result with different runs"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format_source="r"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="r" value="bwa-mem-fastq1.fq"/>
+            <param name="k_select" value="smallk"/>
+            <param name="newQual" value="12 12 0.1"/>
+            <param name="noQual" value="True"/>
+            <param name="stable" value="False"/>
+            <output name="outfile" file="lighter_result1.fq"/>
+        </test>
+        <test>
+            <param name="r" value="bwa-mem-fastq1.fq"/>
+            <param name="k_select" value="bigK"/>
+            <param name="newQual" value="20 14"/>
+            <param name="noQual" value="False"/>
+            <param name="stable" value="True"/>
+            <output name="outfile" file="lighter_result2.fq"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Lighter is a kmer-based error correction method for whole genome sequencing data. Lighter uses sampling
+(rather than counting) to obtain a set of kmers that are likely from the genome. Using this information,
+Lighter can correct the reads containing sequence errors.
+
+    <citations>
+        <citation type="doi">10.1186/s13059-014-0509-9</citation>
+    </citations>
+    </help>
+</tool>