<tool id='scpred_get_feature_space' name='ScPred feature space' version='@TOOL_VERSION@+galaxy0' profile="@PROFILE@">
    <description>Get feature space for training matrix</description>
    <macros>
         <import>scpred_macros.xml</import>
    </macros>
    <expand macro='requirements' />
    <command detect_errors='exit_code'><![CDATA[
        scpred_get_feature_space.R  --input-object '${input_object}'  --prediction-column '${prediction_column}'  --output-path '${output_obj_path}' 

        #if $explained_var_limit
        --explained-var-limit '${explained_var_limit}'
        #end if
        #if $eigenvalue_plot_path
        --eigenvalue-plot-path '${eigenvalue_plot_path}'
        #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='text' name='prediction_column' label='Prediction column' help='Name of the metadata column that contains training labels' />
        <param type='float' name='explained_var_limit' label='Limit of explained variance' value="0.01" help='Threshold to filter principal components based on variance explained' />
    </inputs>
    <outputs>
        <data name='output_obj_path' format='rdata' />
        <data name='eigenvalue_plot_path' format='png' />
    </outputs>
     <tests>
        <test>
            <param name="input_object" value="scPred_object.rds" />
            <param name="prediction_column" value="cell_type2" />
            <output name="output_obj_path" file="scPred_feat_space.rds" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro='citations' />
</tool>