<tool id="scpred_get_std_output" name="Scpred - get output in standard format" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>This method allows to export predicted labels in a standardised format, simplifying downstream analyses.</description>
    <macros>
        <import>scpred_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[ 
        scpred_get_std_output.R --predictions-object "${predictions_object}" --get-scores "${get_scores}" --classifier '${classifier}' --output-table "${output_table}" 
        ]]></command>
    <inputs>
        <param type="data" name="predictions_object" label="Predictions Object" format="rdata" help="Path to the predictions file in text format" />
        <param type="data" name="classifier" label="Classifier object" format="rdata" help="Path to the classifier object used to obtain predictions" />
        <param type="boolean" checked="false" name="get_scores" label="Get scores" help="Boolean: should the prediction scores be included? default: FALSE" />
    </inputs>
    <outputs>
        <data name="output_table" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="predictions_object" value="predicted_data.rds" />
            <param name="get_scores" value="True" />
            <param name="classifier" value="scPred_trained.rds" />
            <output name="output_table" file="scpred_output_tbl.txt" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>