<tool id="extract_bcs.py" name="extract_bcs.py" version="0.1.0">
  <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>