comparison macros.xml @ 5:ff8599e52a55 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf

4:531ff1d417b6

            <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" />
        <param label="the standard deviation of the DNA fragment size"
            name="fragment_sd" type="integer" value="0"/>
    </xml>
</macros>

5:ff8599e52a55

            <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>