--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coords2clnt.xml	Thu Oct 22 09:52:51 2015 -0400
@@ -0,0 +1,45 @@
+<tool id="coords2clnt.py" name="coords2clnt.py" version="1.0">
+  <description>Extract crosslinked nucleotide.</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="stdio" />
+  <stdio>
+    <exit_code level="fatal" range="1:"/>
+  </stdio>
+  <version_command>python coords2clnt.py --version</version_command>
+  <command interpreter="python"><![CDATA[coords2clnt.py
+#if $positional_1 and $positional_1 is not None:
+$positional_1
+#end if
+
+> $default]]></command>
+  <inputs>
+    <param area="false" label="Alignments in bed format." name="positional_1" type="data" format="bed"/>
+  </inputs>
+  <outputs>
+    <data hidden="false" name="default" format="bed"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="positional_1" value="merged_pcr_dupes.bed"/>
+      <output name="default" file="merged_pcr_dupes_clnts.bed"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+Given coordinates of the aligned reads, calculate positions of the crosslinked nucleotides.
+Crosslinked nts are assumed to be one nt upstream of the 5'-end of the read.
+
+Input:
+* bed6 file containing coordinates of aligned reads
+* bed6 file containing coordinates of crosslinking events
+
+Author: Daniel Maticzka
+Copyright: 2015
+License: Apache
+Email: maticzkd@informatik.uni-freiburg.de
+Status: Testing
+]]></help>
+  <expand macro="citations" />
+</tool>