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<tool id="barcode_sort_stacks" name="Barcode sorting for Stacks"  version="2.0.2" force_history_refresh="True">
  <description>Barcode Sorting with Paired-End reads for Stacks</description>

<stdio>
   <exit_code range="1" level="fatal" description="Error in script execution" />
</stdio>

<command interpreter="perl">

barcode_sort.pl $barcode $f1 $f2 $barcoded $nonbarcoded true $barcode_length $cut_site $max_errors

</command>

<inputs>
  <param name="barcode" format="text" type="data" label="Barcode file" />
  <param name="barcode_length" type="integer" value="6" label="Barcode length" />
  <param name="f1" type="data" format="fastq" label="First read FASTQ" />
  <param name="f2" type="data" format="fastq" label="Second read FASTQ" />
  <param name="cut_site" type="text" value="TGCA" label="Cut site" />
  <param name="max_errors" type="integer" value="2" label="Maximum number of errors" />
</inputs>
<outputs>
  <data format="fastq" name="barcoded" label="Barcoded sequences"/>
  <data format="fastq" name="nonbarcoded" label="Non barcoded sequences"/>
</outputs>

<help>

.. class:: infomark

**What it does**

This program takes 2 input sequence files where the barcode can be on either
the 1st or 2nd read (but not both) and sorts all barcoded reads into a single
file and all non-barcoded files into a second file. This separation is needed
for the STACKs program as it does not handle sequences where the barcode is
arbitrarily on the 1st or 2nd read.

--------

**Created by:**

Paul Hohenlohe with changes from Brian Hand.

**Integrated by:**

Tiago Antao


</help>

</tool>