--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bismark_deduplicate/bismark_deduplicate_wrapper.xml	Sat May 06 13:18:09 2017 -0400
@@ -0,0 +1,69 @@
+<tool id="bismark_deduplicate" name="Bismark Deduplicate" version="0.16.3">
+
+    <description>Deduplicates reads mapped by Bismark</description>
+    <!--<version_command>bismark version</version_command>-->
+
+    <requirements>
+        <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="2.1.0">bowtie2</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
+
+    <command interpreter="python">
+<![CDATA[
+        bismark_deduplicate_wrapper.py
+
+        --tool_dir "$__tool_directory__"
+
+        #if str ( $sPaired ) == "single":
+        	-s
+        #else
+        	-p
+        #end if
+
+        --input "$mapping_output"
+
+        --output_report "$output_report"
+        --output_bam "$output_bam"
+
+        ##--log_report "$log_report"
+]]>
+    </command>
+
+    <inputs>
+        <param name="sPaired" type="select" label="Is this library mate-paired?" format="bam">
+            <option value="single">Single-end</option>
+            <option value="paired">Paired-end</option>
+        </param>
+        <param name="mapping_output" type="data" format="bam, sam" label="Submit the resulting bam/sam file from Bismark bisulfite mapper" />
+    </inputs>
+
+    <outputs>
+        <data name="output_bam" format="bam" label="${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)"/>-->
+    </outputs>
+
+    <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>
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