<tool id="scpred_preprocess_data" name="Scpred pre-process" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
    <description>Pre-process input dataset (no train/test split)</description>
    <macros>
        <import>scpred_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        scpred_preprocess_data.R --input-sce-object "${input_sce_object}" --output-matrix-object "${output_mat_object}" 

        #if $norm_counts_slot
        --normalised-counts-slot "${norm_counts_slot}"
        #end if
        #if $output_labels
        --output-labels "${output_labels}"
        #end if

         ]]></command>
    <inputs>
         <param type="data" name="input_sce_object" label="SCE object containing expression data" format="rdata" help="File with serialized SingleCellExperiment object that contains expression matrix" />
         <param type="text" name="norm_counts_slot" optional="true" value="normcounts" label="Normalised counts slot" help="Slot containing normalised counts in input SCE object" />
    </inputs> 
    <outputs>
        <data name="output_mat_object" format="rdata" />
        <data name="output_labels" format="txt" />
    </outputs>
    <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>