<tool id="samtools_split" name="Split" version="1.1">
    <description>BAM dataset on readgroups</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"></expand>
    <expand macro="stdio"></expand>
    <expand macro="version_command"></expand>
    <command><![CDATA[
        samtools split -f 'Read_Group_%!.bam'
        #if $header:
            -u "${output}":"${header}"
        #else:
            -u "${output}"
        #end if
        "${input_bam}"
        ]]></command>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="BAM file" />
        <param name="header" type="data" format="bam,sam" label="Replace header in output file" optional="True" />
     </inputs>
    <outputs>
        <data format="bam" name="output" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="Read_Group_(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true" directory="" />
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_bam" value="phiX.bam" ftype="bam" />
            <output name="output" file="samtools_split_out.bam">
                <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" />
                <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" />
                <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" />
            </output>
        </test>
    </tests>
    <help>
**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"></expand>
</tool>