--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extractSplitReads_BwaMem.xml	Fri Aug 10 11:46:23 2018 -0400
@@ -0,0 +1,109 @@
+<tool id="extractsplitreads_bwamem"
+      name="Extract Split Reads"
+      version="0.1.0">
+
+    <description>from bwaMEM (part of lumpy-sv)</description>
+
+    <requirements>
+        <requirement type="package" version="0.2.14a">lumpy-sv</requirement>
+    </requirements>
+
+    <!-- Not sure yet how to call the command if the lumpy-sv package in bioconda doesn't put the script in an executable location on PATH -->
+
+    <version_command>extractSplitReads_BwaMem | grep ^extractSplitReads_BwaMem | cut -d v -f 2</version_command>
+
+    <command detect_errors="aggressive">
+        <![CDATA[
+            extractSplitReads_BwaMem
+            -i '$input'
+            -n $numSplits
+            $includeDups
+            -m $minNonOverlap
+            > '$output'
+        ]]>
+    </command>
+
+    <inputs>
+
+        <param format="sam" name="input" type="data" label="Sam alignment file" argument="--infile"/>
+
+        <param name="numSplits"
+               label="numSplits"
+               argument="--numSplits"
+
+               type="integer"
+               value="2"
+
+               help="The maximum number of split-read mappings to allow per read. Reads with more are excluded." />
+
+        <param name="includeDups"
+               label="includeDups"
+               argument="--includeDups"
+
+               type="boolean"
+               truevalue="--includeDups"
+               falsevalue=""
+               checked="no"
+               value="false"
+
+               help="Include alignments marked as duplicates." />
+
+        <param name="minNonOverlap"
+               label="minNonOverlap"
+               argument="--minNonOverlap"
+
+               type="integer"
+               value="20"
+
+               help="Minimum non-overlap between split alignments on the query." />
+
+    </inputs>
+    <outputs>
+        <data format="sam" name="output" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="JS01-BWA-MEM.splitters.sam"/>
+            <output name="output" file="JS01-BWA-MEM.splitters.out.sam"/>
+        </test>
+        <test>
+            <param name="input" value="pe.pos_sorted.sam"/>
+            <output name="output" file="pe.pos_sorted.out.sam"/>
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+
+Usage: `extractSplitReads_BwaMem -i <file>`
+
+extractSplitReads_BwaMem v0.1.0
+
+Author: Ira Hall
+
+Description: Get split-read alignments from bwa-mem in lumpy compatible format. Ignores reads marked as duplicates.
+
+Works on read or position sorted SAM input. Tested on bwa mem v0.7.5a-r405. 
+
+
+Options:
+  -h, --help            show this help message and exit
+  -i FILE, --inFile=FILE
+                        A SAM file or standard input (-i stdin).
+  -n INT, --numSplits=INT
+                        The maximum number of split-read mappings to allow per
+                        read. Reads with more are excluded. Default=2
+  -d, --includeDups     Include alignments marked as duplicates. Default=False
+  -m INT, --minNonOverlap=INT
+                        minimum non-overlap between split alignments on the
+                        query (default=20)
+
+        ]]>
+    </help>
+
+    <citations>
+        <citation type="doi">doi:10.1186/gb-2014-15-6-r84</citation>
+    </citations>
+
+</tool>