<tool id="scmap_scmap_cluster" name="Scmap cluster projection" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>projects one dataset to another</description>
    <macros>
        <import>scmap_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        scmap-scmap-cluster.R --index-object-file '$index_single_cell_experiment' --projection-object-file '$project_single_cell_experiment' --threshold '$threshold' --output-object-file '$output_single_cell_experiment' --output-text-file '$output_txt'
    ]]></command>
    <inputs>
        <param type="data" name="index_single_cell_experiment" label="Index SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features' and 'scmap index clusters', onto which another dataset will be projected." />
        <param type="data" name="project_single_cell_experiment" label="SingleCellExperiment object to project" format="rdata" help="File with serialized SingleCellExperiment object to project onto the index'" />
        <param name="threshold" type="float" label="Threshold" value="0.7" help="Threshold on similarity (or probability for SVM and RF)." />
    </inputs>
    <outputs>
        <data name="output_single_cell_experiment" format="rdata" label="${tool.name} on ${on_string}: RDS object"/>
        <data name="output_txt" format="tabular" label="${tool.name} on ${on_string}: table"/>
    </outputs>
    <tests>
        <test>
            <param name="index_single_cell_experiment" value="index_cluster.rds" ftype="rdata"/>
            <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
            <output name="output_single_cell_experiment">
                <assert_contents>
                    <has_size value="6100k" delta="500k"/>
                </assert_contents>
            </output>
            <output name="output_txt">
                <assert_contents>
                    <has_n_lines n="91"/>
                    <has_text text="zygote"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>