--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_bcs.xml	Thu Oct 22 09:52:51 2015 -0400
@@ -0,0 +1,44 @@
+<tool id="extract_bcs.py" name="extract_bcs.py" version="1.0">
+  <description>Extract barcodes using pattern.</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="stdio" />
+  <version_command>python extract_bcs.py --version</version_command>
+  <command interpreter="python"><![CDATA[
+extract_bcs.py
+#if $positional_1 and $positional_1 is not None:
+$positional_1
+#end if
+
+#if $positional_2 and $positional_2 is not None:
+$positional_2
+#end if
+
+> $default]]></command>
+  <inputs>
+    <param area="false" label="Barcoded sequences." name="positional_1" type="data" format="fastq"/>
+    <param area="false" label="Pattern of barcode nucleotides starting at 5'-end. X positions will be moved to the header, N positions will be kept." name="positional_2" type="text"/>
+  </inputs>
+  <outputs>
+    <data hidden="false" name="default" format="fastq" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="positional_1" value="reads.fastq"/>
+      <param name="positional_2" value="XXXNNXXX"/>
+      <output name="default" file="result.fastq"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+Exract barcodes from a FASTQ file according to a user-specified pattern.
+
+Author: Daniel Maticzka
+Copyright: 2015
+License: Apache
+Email: maticzkd@informatik.uni-freiburg.de
+Status: Testing
+]]></help>
+  <expand macro="citations" />
+</tool>