--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_scidx.xml	Tue Nov 24 08:13:56 2015 -0500
@@ -0,0 +1,50 @@
+<tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.0">
+    <description></description>
+    <command>
+        <![CDATA[
+            python $__tool_directory__/bam_to_scidx.py
+            -j $__tool_directory__/BAMtoIDX.jar
+            -b "$input_bam"
+            -i "${input_bam.metadata.bam_index}"
+            -r $read
+            -o "$output"
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_bam" type="data" format="bam" label="BAM file" help="BAM file must be sorted and indexed" />
+        <param name="read" type="select" label="Read to output">
+            <option value="0" selected="True">Read1</option>
+            <option value="1">Read2</option>
+            <option value="2">Combined</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="scidx" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="input.bam" ftype="bam" />
+            <param name="read" value="0" />
+            <output name="output" file="output.scidx" />
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by
+tools within the Chip-exo Galaxy flavor.  The Chip-exo Galaxy flavor is used by the Center for
+Eukaryotic Gene Regulation labs at The Pennsylvania State University.  ScIdx files are 1-based.
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{None,
+            author = {None},
+            title = {None},
+            year = {None},
+            eprint = {None},
+            url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
+        }</citation>
+    </citations>
+</tool>