<tool id="b2b_count_mapped_reads" name="Count mapped reads" version="0.001">

    <description>Count reads uniquely mapped to each reference sequence</description>

    <!-- ***************************************************************** -->

    <requirements>
        <!-- ncurses needs to be explicitly pulled from conda-forge for samtools to work -->
        <requirement type="package" version="6.1">ncurses</requirement>
        <requirement type="package" version="1.9">samtools</requirement>
    </requirements>

    <!-- ***************************************************************** -->

    <version_command>echo "0.001"</version_command>

    <!-- ***************************************************************** -->

    <command detect_errors="aggressive">
    <![CDATA[

    #if $uniq:
        samtools view -F 0x04 -F 0x100 -F 0x800 $in
    #else
        samtools view -F 0x04 $in
    #end if
    | cut -f3
    | sort
    | uniq -c
    | awk -v OFS='\t' '{print $2,$1}'
    > $out

    ]]>
    </command>

    <!-- ***************************************************************** -->

    <inputs>
        <param name="in" type="data" format="bam" label="Read mapping" help="BAM format" />
        <param name="uniq" type="boolean" checked="True" label="Exclude ambiguous mappings" />
    </inputs>

    <!-- ***************************************************************** -->

    <outputs>
        <data name="out" format="tabular" label="Read counts" />
    </outputs>

    <!-- ***************************************************************** -->

    <tests>
        <test>
            <param name="in" value="b2c.bam" ftype="bam" />
            <output name="out" file="b2c.counts" compare="diff" />
        </test>
    </tests>

    <!-- ***************************************************************** -->

    <help>

    `count_mapped_reads` is a Galaxy-only utility from BASE2BIO that simply
    reports the number of reads mapped to each sequence from a BAM input file.

    </help>

    <!-- ***************************************************************** -->

    <citations>
    </citations>

</tool>