<tool id="bamtools_split_mapped" name="Split BAM by Mapped" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description></description>
    <macros>
          <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
        <![CDATA[
            ln -s '${input_bam}' 'localbam.bam' &&
            ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' &&
            bamtools split -mapped
            -in localbam.bam
            -stub split_bam
        ]]>
    </command>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="BAM dataset to split by mapped/unmapped"/>
    </inputs>
    <outputs>
        <data format="bam" name="mapped" label="${input_bam.name} mapped" from_work_dir="split_bam.MAPPED.bam" />
        <data format="bam" name="unmapped" label="${input_bam.name} unmapped" from_work_dir="split_bam.UNMAPPED.bam" />
    </outputs>
    <tests>
        <test>
            <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
            <output name="mapped" file="split_bam.MAPPED.bam"  compare="sim_size" delta="200" />
            <output name="unmapped" file="split_bam.UNMAPPED.bam"  compare="sim_size" delta="200" />
        </test>
    </tests>
    <help>
**What is does**

BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).

-----

.. class:: warningmark


**How it works**

Splits the input BAM file into 2 output files named (MAPPED) and (UNMAPPED) containing mapped and unmapped reads, respectively.

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.. class:: infomark

**More information**

Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki

    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btr174</citation>
    </citations>
</tool>