<macros>
    <token name="@TOOL_VERSION@">0.0.1</token>
    <token name="@VERSION_SUFFIX@">2</token>
	<token name="@PROFILE@">22.01</token>

    <xml name="bayestme_requirements">
        <requirements>
            <container type="docker">jeffquinnmsk/bayestme:0a7cde6acac2ffc34e8ad00b7fab75f869d80de2</container>
        </requirements>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1016/j.cels.2023.06.003</citation>
        </citations>
    </xml>
	
	<xml name="filter_genes_options" >
	    
	    <param argument="--n-top-by-standard-deviation" type="integer" value = "1000" optional="false" label="Use the top N genes with the highest spatial variance"/>
		
	    <!-- Additional filtering options -->
		<section name="additional_filtering_options" title="Additional Filtering Parameters" expanded="false"> 
		    <param argument="--spot-threshold" optional="true" type="float" label="Filter genes appearing in greater than the provided threshold of tissue spots"/>
			<param argument="--filter-ribosomal-genes" type="boolean" checked="false" label="Filter ribosomal genes (based on gene name regex)"/>
		</section>
	    
	</xml>
	
</macros>
