<tool id="scmap_select_features" name="scmap select features" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>finds the most informative features (genes/transcripts) for projection.</description>
    <macros>
        <import>scmap_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${input_single_cell_experiment}.preprocessed" && scmap-select-features.R --input-object-file "${input_single_cell_experiment}.preprocessed" --n-features '$n_features' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
    ]]></command>
    <inputs>
        <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object" />
        <param name="n_features" type="integer" label="Number of features" value="500" help="Number of features to be selected" />
    </inputs>
    <outputs>
        <data name="output_single_cell_experiment" format="rdata" />
        <data name="plot" format="png" />
    </outputs>
    <tests>
        <test>
            <param name="input_single_cell_experiment" value="test_sce.rds" ftype="rdata"/>
            <output name="output_single_cell_experiment" file="select_features.rds" compare="sim_size"/>
            <output name="plot" file="select_features.png" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>