<macros>
    <!-- The documentation says a v1.0 is in the works
         but the repository has seen no changes for 3-4 years -->
    <token name="@VERSION@">0.17.17</token>
    <token name="@SAMTOOLS_OPTS@"><![CDATA[
    --samtools-threads \${GALAXY_SLOTS:-1}
    --samtools-memory \${GALAXY_MEMORY_MB:-100}
    ]]></token>
    <token name="@LOOMOUT@"><![CDATA[
    -o "."
    -e "output"
    ]]></token>
    
    <xml name="bcffile" >
        <param argument="-b" type="data" format="tabular,txt" optional="true"
               label="Barcodes file to filter BAM"
               help="If -bcfile is not specified the file will be searched in the default position outputted by 'dropest_bc_correct'. Otherwise an error will be thrown" />
    </xml>
    <xml name="loomdtype" token_16_selected="true" token_32_selected="false" >
        <param argument="-t" type="select" optional="true"
               label="Datatype of Loom layers"
               help="The dtype of the loom file layers - if more than 6000 molecules/reads per gene per cell are expected set uint32
                     to avoid truncation" >
            <option value="uint16" selected="@16_SELECTED@">uint16</option>
            <option value="uint32" selected="@32_SELECTED@">uint32</option>
        </param>
    </xml>
    <xml name="repmask" >
        <param argument="-m" type="data" format="gtf" optional="true"
               label="Intervals to mask" />
    </xml>
    <xml name="notuniquemappings" >
        <param argument="-M" type="boolean" truevalue="-M" falsevalue="" checked="false"
               label="Consider not unique mappings?" help="(not recommended)" />
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/s41586-018-0414-6</citation>
        </citations>
    </xml>
    <xml name="edam">
        <edam_topics>
            <edam_topic>topic_3512</edam_topic>
            <edam_topic>topic_3320</edam_topic>
        </edam_topics>
        <edam_operations>
            <edam_operation>operation_3800</edam_operation>
        </edam_operations>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@" >velocyto.py</requirement>
        </requirements>
    </xml>
</macros>