<tool id="pe_histogram" name="Paired-end histogram" version="1.0.0">
    <description>of insert size frequency</description>
    <requirements>
        <requirement type="package" version="8.0.45">java-jdk</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range=":-1" />
        <exit_code range="1:" />
        <!-- Check stderr in case the return code has not been set -->
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <command>
        <![CDATA[
            ln -s "${input_bam}" "localbam.bam" &&
            ln -f -s "${input_bam.metadata.bam_index}" "localbam.bam.bai" &&
            java -jar $__tool_directory__/PEHistogram.jar
            -B "localbam.bam"
            -I "localbam.bam.bai"
            #if str($lower_limit) != '':
                -l $lower_limit
            #end if
            #if str($upper_limit) != '':
                -u $upper_limit
            #end if
            -p "$output1"
            -t "$output2" 1>/dev/null
        ]]>
    </command>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="BAM file" />
        <param name="lower_limit" type="integer" value="" optional="True" min="0" label="Lower bp limit (optional)" help="The lower bp limit on insert size for calculating the histogram."/>
        <param name="upper_limit" type="integer" value="" optional="True" min="0" label="Upper bp limit (optional)" help="The upper bp limit on insert size for calculating the histogram." />
    </inputs>
    <outputs>
        <data name="output1" format="png" />
        <data name="output2" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input_bam" value="input.bam" ftype="bam" />
            <output name="output1" file="output1.png" ftype="png" compare="sim_size" />
            <output name="output2" file="output1.tabular" ftype="tabular" compare="contains" />
        </test>
        <test>
            <param name="input_bam" value="input.bam" ftype="bam" />
            <param name="lower_limit" value="200" />
            <param name="upper_limit" value="300" />
            <output name="output1" file="output2.png" ftype="png" compare="sim_size" />
            <output name="output2" file="output2.tabular" ftype="tabular" compare="contains" />
        </test>
    </tests>
    <help>

**What it does**

Produces an insert size histogram and basic statistics for a paired-end BAM file.  Two outputs are produced:

- a png image consisting of the histogram of the insert size frequency
- a tabular file containing the alignment statistics

-----

**Options**

* **Lower bp limit** - the lower bp limit on insert size for calculating the histogram.
* **Upper bp limit** - the upper bp limit on insert size for calculating the histogram.

    </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>