--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_scidx.xml	Sat Dec 12 15:46:03 2015 -0500
@@ -0,0 +1,63 @@
+<tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.0">
+    <description></description>
+    <command>
+        <![CDATA[
+            ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" &&
+            java -jar $__tool_directory__/BAMtoscIDX.jar -b "$input_bam" -i "${input_bam}.bai" -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_bam" type="data" format="bam" label="BAM file" />
+        <param name="require_proper_mate_pairing" type="select" label="Require proper mate-pairing?" help="Required if filtering by insert size for single-end Reqd 1 (below)." >
+            <option value="1" selected="True">Yes</option>
+            <option value="0">No</option>
+        </param>
+        <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>
+        <param name="min_insert_size" type="integer" value="" optional="True" min="0" label="Minimum insert size to output" help="Will not filter out single-end Read 1 unless proper mate-pairing is required (above)."/>
+        <param name="max_insert_size" type="integer" value="" optional="True" min="0" label="Maximum insert size to output" help="Will not filter out single-end Read 1 unless proper mate-pairing is required (above)." />
+    </inputs>
+    <outputs>
+        <data name="output" format="scidx" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_bam" value="input.bam" ftype="bam" />
+            <param name="require_proper_mate_pairing" value="1" />
+            <param name="read" value="0" />
+            <output name="output" file="output.scidx" lines_diff="1" ftype="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.  ScIdx files are 1-based.  The format consists of 5 columns: the chromosome,
+the position of the genomic coordinate, the number of tags on the forward strand, the number of tags on
+the reverse strand and the number of total tags on the position.  With pair-end reads, only the 5’ end of
+READ1 will be used to create the ScIdx data file.  Tools that use this format include GeneTrack and MultiGPS.
+
+-----
+
+**Options**
+
+* **Require proper mate-pairing?** - Select **Yes** to require proper mate paring.  Filtering by insert size parameters will not filter out single-end Read 1 unless proper mate-pairing is required.
+* **Minimum insert size to output** - Insert size below the minimum will be filtered from the results, but single-end Read 1 will not be filtered unless proper mate-pairing is required.
+* **Maximum insert size to output** - Insert size above the maximum will be filtered from the results, but single-end Read 1 will not be filtered unless proper mate-pairing is required.
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{None,
+            author = {Lai, William},
+            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>