<tool id="scmap_index_cluster" name="scmap index clusters" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>calculates centroids of each cell type and merges them into a single table</description>
    <macros>
        <import>scmap_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds && scmap-index-cluster.R --input-object-file sce_object_preprocessed.rds --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
        #if $train_id
        --train-id '${train_id}' 
        #end if
    ]]></command>
    <inputs>
        <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features'" />
        <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" />
        <param name="cluster_col" type="text" label="Cluster column" value="cell_type1" help="Column name in the 'colData' slot of the SingleCellExperiment object containing the cell classification information." />
    </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="select_features.rds" ftype="rdata"/>
            <output name="output_single_cell_experiment" file="index_cluster.rds" compare="sim_size"/>
            <output name="plot" file="index_cluster.png"/>
        </test>
    </tests>
    <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>