<tool id="bctools_convert_to_binary_barcode" name="Create binary barcodes" version="@VERSION@">
    <description>from regular barcodes.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        convert_bc_to_binary_RY.py
        '$barcodes'
        > '$barcodes_ry'
    ]]></command>
    <inputs>
        <param name="barcodes" type="data" format="fastq" label="FASTQ file to convert"/>
    </inputs>
    <outputs>
        <data name="barcodes_ry" format="fastq"/>
    </outputs>
    <tests>
        <test>
            <param name="barcodes" value="extracted_bcs.fastq"/>
            <output name="barcodes_ry" file="converted_bcs.fastq"/>
        </test>
    </tests>
    <help><![CDATA[

bctools - Create binary barcodes from regular barcodes
======================================================

This tool converts standard nucleotide codes to the IUPAC nucleotide codes used for binary barcodes.
A and G are converted to nucleotide code R. T, U and C are converted to Y.

Input
-----

The input for this tool is a FASTQ file.

Output
------

This tool produces a single FASTQ file containing the converted barcodes.

    ]]></help>
    <expand macro="citations"/>
</tool>