<tool id="fgbio_sort_bam" name="fgbio SortBam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
    <description>Sorts a SAM or BAM file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command>fgbio --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        fgbio SortBam 
        --input '$input'
        #if $sort_order
            --sort-order=$sort_order
        #end if
        --output '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="unsorted.bam,bam,sam" label="SAM/BAM to sort"/>
        <expand macro="sam_sort_order" />
    </inputs>
    <outputs>
        <data name="output" format="unsorted.bam" >
            <!--
            <expand macro="sort_order_change_format" />
            -->
        </data>
    </outputs>
    <help><![CDATA[
**fgbio SortBam**

Sorts a SAM or BAM file. Several sort orders are available:

    - Coordinate: sorts reads by their reference sequence and left-most aligned coordinate
    - Queryname: sort the reads by their query (i.e. read) name
    - Random: sorts the reads into a random order. The output is deterministic for any given input. and several
    - RandomQuery: sorts the reads into a random order but keeps reads with the same queryname together. The ordering is deterministic for any given input.

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