comparison barcode_sort.xml @ 0:d838c6a2ec0f draft

planemo upload commit 75d88a8a93e8cd3acb00103bf6a7a07649d17c70

0:d838c6a2ec0f

<tool id="barcode_sort_stacks" name="Barcode sorting for Stacks"  version="1.0.0" force_history_refresh="True">
  <description>Run the STACKS populations program</description>


<requirements>
    <requirement type="package" version="5.18">perl</requirement>
</requirements>



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

<command interpreter="perl">

barcode_sort.pl $barcode $f1 $f2 $barcoded $nonbarcoded

</command>

<inputs>
  <param name="barcode" format="txt" type="data" label="Barcode file 1" />
  <param name="f1" format="fastq" label="First reads" />
  <param name="f2" format="fastq" label="Second reads" />
</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>

<citations>
</citations>
</tool>