<tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.0">
    <description></description>
    <command>
        <![CDATA[
            python $__tool_directory__/bam_to_scidx.py
            -j $__tool_directory__/BAMtoIDX.jar
            -b "$input_bam"
            -i "${input_bam.metadata.bam_index}"
            -r $read
            -o "$output"
        ]]>
    </command>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="BAM file" help="BAM file must be sorted and indexed" />
        <param name="read" type="select" label="Read to output">
            <option value="0" selected="True">Read1</option>
            <option value="1">Read2</option>
            <option value="2">Combined</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="scidx" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="input.bam" ftype="bam" />
            <param name="read" value="0" />
            <output name="output" file="output.scidx" />
        </test>
    </tests>
    <help>

**What it does**

Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by
tools within the Chip-exo Galaxy flavor.  The Chip-exo Galaxy flavor is used by the Center for
Eukaryotic Gene Regulation labs at The Pennsylvania State University.  ScIdx files are 1-based.

    </help>
    <citations>
        <citation type="bibtex">
            @unpublished{None,
            author = {None},
            title = {None},
            year = {None},
            eprint = {None},
            url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
        }</citation>
    </citations>
</tool>