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scater-manual-filter.xml
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scater-manual-filter.xml
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<tool id="scater-manual-filter" name="Scater: manually filter SCE" version="@TOOL_VERSION@">
<description>Filter SCE with user-defined parameters</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements" />
<command detect_errors="exit_code"><![CDATA[
'$__tool_directory__/scater-manual-filter.R'
-i '$input_sce'
#if str($detection_limit).strip():
--detection-limit '$detection_limit'
#end if
#if str($library_size).strip():
--library-size '$library_size'
#end if
#if str($percent_counts_MT).strip():
--percent-counts-MT '$percent_counts_MT'
#end if
-o '$output_sce'
]]></command>
<inputs>
<param name="input_sce" type="data" format="rdata.sce" label="Input SingleCellExperiment dataset" />
<param name="detection_limit" argument="--detection-limit" type="text" optional="true" label="Number of reads mapped to a gene for it to be counted as expressed" help="Raising this number will raise the stringency and may lower the number of expressed genes" />
<param name="library_size" argument="--library-size" type="text" optional="true" label="Minimum library size (mapped reads) to filter cells on" help="Raising this number will raise the stringency and may lower the number of included cells" />
<param name="percent_counts_MT" argument="--percent-counts-MT" type="text" optional="true" label="Maximum % of mitochondrial genes expressed per cell." help="Cells that exceed this value will be filtered out" />
</inputs>
<outputs>
<data name="output_sce" format="rdata.sce" label="${tool.name} on ${on_string}" />
</outputs>
<tests>
<test>
<param name="input_sce" value="scater_qcready_sce.rds" ftype="rdata.sce" />
<param name="detection_limit" value="4" />
<param name="library_size" value="100000" />
<param name="percent_counts_MT" value="33" />
<output name="output_sce" file="scater_manual_filtered.rds" compare="sim_size" />
</test>
</tests>
<help><![CDATA[
Manually filter SingleCellExperiment with user-defined parameters for single-cell RNA-seq analysis using Scater.
]]></help>
<expand macro="citations" />
</tool>