annotate macros.xml @ 1:7bc75dd0f782 draft

planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/helixer commit e516933a2c3aa6bcd336a0b5c072893fe9019dd9

<macros>
    <token name="@TOOL_VERSION@">0.3.2</token>

    <xml name="citation">
        <citations>
            <citation type="doi">10.1101/2023.02.06.527280</citation>
            <citation type="doi">10.1093/bioinformatics/btaa1044</citation>
        </citations>
    </xml>

    <xml name="requirements">
        <container type="docker">gglyptodon/helixer-docker:helixer_v@TOOL_VERSION@_cuda_11.8.0-cudnn8</container>
    </xml>
    
    <xml name="subseq" tokens="length,offset,offsetlen">
        <param argument="--subsequence-length" type="integer" min="0" max="213840" value="@LENGTH@" label="Subsequence length: how much of the genome the Neural Network can see at once" help="Should ideally be comfortably longer than the typical gene. For genomes with large genes (>20kpb) it is recommended to increase this parameter."></param>
        <conditional name="option_overlap">
            <param name="use_overlap" type="select" label="Enable overlapping step after predictions" help="This step combines predictions made on each subsequences, to improve quality near start and end of subsequences">
                <option value="true" selected="true">Yes</option>
                <option value="false">No</option>
            </param>
            <when value="true">
                <param argument="--overlap-offset" type="integer" min="0" value="@OFFSET@" label="Overlap offset" help="Smaller values may lead to better predictions but will take longer. The subsequence length should be evenly divisible by this value."/>
                <param argument="--overlap-core-length" type="integer" min="0" value="@OFFSETLEN@" label="Overlap core length" help="Predicted subsequences will be cut to this length to increase prediction quality. Smaller values may lead to better predictions but will take longer. Has to be smaller than subsequence_length."/>
            </when>
            <when value="false"/>
        </conditional>
    </xml>
</macros>