--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coords2clnt.xml	Tue Nov 14 05:52:26 2017 -0500
@@ -0,0 +1,45 @@
+<tool id="bctools_extract_crosslinked_nucleotides" name="Get crosslinked nucleotides" version="@VERSION@">
+    <description>from full alignments</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        coords2clnt.py
+        '$alignment_coordinates'
+        > '$crosslinking_coordinates'
+    ]]></command>
+    <inputs>
+        <param name="alignment_coordinates" type="data" format="bed" label="Alignments in BED format"/>
+    </inputs>
+    <outputs>
+        <data name="crosslinking_coordinates" format="bed"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="alignment_coordinates" value="merged_pcr_dupes.bed"/>
+            <output name="crosslinking_coordinates" file="merged_pcr_dupes_clnts.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+bctools - Get crosslinked nucleotides from full alignments
+==========================================================
+
+Given coordinates of aligned reads in BED format, calculate positions of the
+crosslinked nucleotides. Crosslinked nts are assumed to be one nt upstream of
+the 5'-end of the read.
+
+Input
+-----
+
+* six column BED file containing coordinates of aligned reads
+
+Output
+------
+
+* six column BED file containing coordinates of crosslinking events
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>