<tool id="scpred_predict_labels" name="Scpred predict" version="@TOOL_VERSION@+galaxy3">
    <description>Make cell type predictions using trained model.</description>
     <macros>
        <import>scpred_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        scpred_predict.R --input-object "${input_object}" --pred-data "${pred_data}" --output-path "${output_tbl_path}"  

        #if $test_labels
        --test-labels "${test_labels}" 
        #end if
        #if $cell_types_column
        --cell-types-column "${cell_types_column}"
        #end if
        #if $plot_path
        --plot-path "${plot_path}"
        #end if
        #if $confusion_table
        --confusion-table "${confusion_table}"
        #end if

        ]]></command>
    <inputs>
        <param type="data" name="input_object" label="Input SCE object" format="rdata" help="Input SCE object in .rds format" />
        <param type="data" name="pred_data" label="Matrix with query data" format="rdata" help="Path to the input prediction matrix in .rds format"/>
        <param type="data" name="test_labels" optional="true" format="txt" label="Test labels" help="Path to the test labels file for evalutation of model performance in text format" />
        <param type="text" name="cell_types_column" value="cell_type2" optional="true" label="Cell types column name" help="Column name of true labels in provided metadata file" />
    </inputs>
    <outputs>
        <data name="output_tbl_path" format="txt" />
        <data name="plot_path" format="txt" />
        <data name="confusion_table" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="input_object" value="scPred_trained.rds" />
            <param name="pred_data" value="test_matrix.mtx" />
            <param name="test_labels" value="test_metadata.txt" />
            <output name="output_tbl_path" file="predictions_table.txt" compare="sim_size"/>
        </test>
    </tests>
     <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>