<tool id="samtools_split" name="Samtools split" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>BAM dataset on readgroups</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
    @ADDTHREADS@
    samtools split -f 'Read_Group_%!.bam'
    #if $header:
        -u '${output}:${header}'
    #else:
        -u '${output}'
    #end if
    -@ \$addthreads
    '$input_bam'
    ]]></command>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="BAM file" />
        <param name="header" type="data" format="bam,sam" optional="True" label="Replace header in output file" />
     </inputs>
    <outputs>
        <data name="output" format="bam" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="Read_Group_(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true" directory="" assign_primary_output="false"/>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_bam" value="phiX.bam" ftype="bam" />
            <output name="output">
                <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" lines_diff="4" />
                <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" lines_diff="4" />
                <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" lines_diff="4" />
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Splits BAM files on readgroups.

This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset.
    ]]></help>
    <expand macro="citations"/>
</tool>