<macros>
    <token name="@WRAPPER_VERSION@">2014.11.03.0</token>
    <xml name="stdio">
        <stdio>
            <!-- Anything other than zero is an error -->
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <!-- In case the return code has not been set propery check stderr too -->
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
    </xml>
    <xml name="aln">
        <param type="boolean" label="output ALN alignment file (-a)" name="aln"
            truevalue="-a" falsevalue="" />
    </xml>
    <xml name="sam">
        <param type="boolean" label="output SAM alignment file (-s)" name="sam"
            truevalue="-s" falsevalue="" />
    </xml>

    <xml name="rndSeed">
        <param label="specify a fixed, random seed for the simulation"
            help="Use -1 to request a random seed (-r)" name="rndSeed"
            type="integer" value="-1" optional="true" />
    </xml>

    <xml name="citation">
        <citations>
            <citation type="doi">10.1093/bioinformatics/btr708</citation>
        </citations>
    </xml>

    <xml name="amplicon">
        <conditional name="amplicon">
            <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" />
            <when value="amplicon_true">
                <param label="number of reads per amplicon (for 5'end amplicon sequencing)" name="reads_per_amplicon" type="integer" value="0"/>
            </when>
            <when value="amplicon_false">
            </when>
        </conditional>
    </xml>

    <xml name="amplicon_pair">
        <conditional name="amplicon">
            <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" />
            <when value="amplicon_true">
                <param label="number of read pairs per amplicon (for two-end amplicon sequencing)" name="read_pairs_per_amplicon" type="integer" value="0"/>
            </when>
            <when value="amplicon_false">
            </when>
        </conditional>
    </xml>

    <xml name="frag_len_sd">
        <param label="the average DNA fragment size"
            name="fragment_size" type="integer" value="200" minimum="101" />
        <param label="the standard deviation of the DNA fragment size"
            name="fragment_sd" type="integer" value="0"/>
    </xml>
</macros>