<tool id="paired_end_cross_plot" name="Paired-end cross plot" version="1.0.0">
    <description></description>
    <command>
        <![CDATA[
            java -jar $__tool_directory__/pairedendCrossPlot.jar
            -f "$input1"
            -r "$input2"
            -w $window_size
            -o "$output" 1>/dev/null
        ]]>
    </command>
    <inputs>
        <param name="input1" type="data" format="scidx" label="Read 1 ScIdx file" />
        <param name="input2" type="data" format="scidx" label="Read 2 ScIdx file" />
        <param name="window_size" type="integer" value="500" min="1" label="Size of window upstream and downstream around the reference point in base pairs" />
    </inputs>
    <outputs>
        <data name="output" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="input1.scidx" ftype="scidx"/>
            <param name="input2" value="input2.scidx" ftype="scidx"/>
            <param name="window_size" value="500"/>
            <output name="output" file="output1.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="input1" value="input3.scidx" ftype="scidx"/>
            <param name="input2" value="input4.scidx" ftype="scidx"/>
            <param name="window_size" value="500"/>
            <output name="output" file="output2.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>

**What it does**

Produces a frequency histogram of the relative occurrence of Read2 5' ends relative to the
start of every Read1 5' end in a user-specified coordinate window.

-----

**Options**

* **Window Size** - sets the size of the window upstream and downstream around the reference point in base pairs.

    </help>
    <citations>
        <citation type="bibtex">
            @unpublished{None,
            author = {Lai, William},
            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>