<tool id="fgbio_sort_fastq" name="fgbio SortFastq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
    <description>Sorts the records in a FASTQ file based on the lexicographic ordering of their read names</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command>fgbio --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        fgbio SortFastq
        --input '$input'
        #if $input.is_of_type("fastq.gz", "fastqsanger.gz")
            --output output.fastq.gz
            && cp output.fastq.gz '$output'
        #else
            --output output.fastq
            && cp output.fastq '$output'
        #end if
    ]]></command>
    <inputs>
        <param name="input" type="data" format="fastq,fastq.gz" label="fastq file to be sorted"/>
    </inputs>
    <outputs>
        <data name="output" format_source="input" label="Sorted ${input.name}"/>
    </outputs>
    <help><![CDATA[
**fgbio SortFastq**

Sorts a FASTQ file. Sorts the records in a FASTQ file based on the lexicographic ordering of their read names. Input and output files can be either uncompressed or gzip-compressed.

http://fulcrumgenomics.github.io/fgbio/tools/latest/SortFastq.html
    ]]></help>
    <expand macro="citations" />
</tool>