<macros>
    <token name="@WRAPPER_VERSION@">2016.06.05</token>

    <xml name="requirements">
      <requirements>
        <requirement type="package" version="2016.06.05">art</requirement>
        <yield/>
      </requirements>
    </xml>

    <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 name="aln" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Output ALN alignment file" />
    </xml>
    <xml name="sam">
        <param name="sam" argument="-s" type="boolean" truevalue="-s" falsevalue="" label="Output SAM alignment file" />
    </xml>

    <xml name="rndSeed">
        <param name="rndSeed" argument="-r" type="integer" value="-1" optional="true" label="Fixed random seed for the simulation"
            help="Use -1 to request a random seed" />
    </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" truevalue="amplicon_true" falsevalue="amplicon_false" label="Run Amplicon Sequencing Simulation" />
            <when value="amplicon_true">
                <param name="reads_per_amplicon" type="integer" value="0" label="Number of reads per amplicon (for 5'end amplicon sequencing)" />
            </when>
            <when value="amplicon_false" />
        </conditional>
    </xml>

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

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