--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bismark_deduplicate_wrapper.xml	Wed Aug 22 08:09:42 2018 -0400
@@ -0,0 +1,66 @@
+<tool id="bismark_deduplicate" name="Bismark Deduplicate" version="0.20.0" profile="18.01">
+    <description>Deduplicates reads mapped by Bismark</description>
+    <requirements>
+        <requirement type="package" version="0.20.0">bismark</requirement>
+        <requirement type="package" version="1.8">samtools</requirement>
+        <requirement type="package" version="2.3.4.2">bowtie2</requirement>
+    </requirements>
+    <command><![CDATA[
+        python '$__tool_directory__/bismark_deduplicate_wrapper.py'
+
+        --single_or_paired $sPaired
+
+        --input '$mapping_output'
+        --output_report '$output_report'
+        --output_bam '$output_bam'
+        #if $separate_logfile:
+           --log_report '$log_report'
+        #end if
+]]>
+    </command>
+    <inputs>
+        <param name="sPaired" type="select" label="Is this library mate-paired?">
+            <option value="single">Single-end</option>
+            <option value="paired">Paired-end</option>
+        </param>
+        <param name="mapping_output" type="data" format="qname_input_sorted.bam,bam"
+               label="Submit the resulting bam/sam file from Bismark bisulfite mapper"/>
+        <param name="separate_logfile" type="boolean" truevalue="true" falsevalue="false" checked="False"
+               label="Create a separate logfile, otherwise logs are added to the dataset info."/>
+    </inputs>
+
+    <outputs>
+        <data name="output_bam" format="qname_sorted.bam"
+              label="${tool.name} on ${on_string}: deduplicated mapped reads"/>
+        <data name="output_report" format="txt" label="${tool.name} on ${on_string}: deduplication report"/>
+        <data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)">
+            <filter>( separate_logfile is True )</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="sPaired" value="single"/>
+            <param name="mapping_output" value="mapped_reads.bam" ftype="qname_sorted.bam"/>
+            <output name="output_bam" file="dedup_reads.bam" ftype="qname_sorted.bam"/>
+            <output name="output_report" file="dedup_report.txt" ftype="txt"/>
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+**What it does**
+
+	| This tool is supposed to remove alignments to the same position in the genome from the Bismark mapping output (both single and paired-end SAM files), which can arise by e.g. excessive PCR amplification. If sequences align to the same genomic position but on different strands they will be scored individually.
+	|
+	| Note that deduplication is not recommended for RRBS-type experiments!
+	|
+	| For single-end alignments only use the start-coordinate of a read will be used for deduplication.
+	| For paired-end alignments the start-coordinate of the first read and the end coordinate of the second read will be used for deduplication.
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btr167</citation>
+    </citations>
+</tool>