<tool id="garnett_get_std_output" name="Garnett - get standard output" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>Get final output in standard format to allow for downstream analysis of predicted labels by tools of the EBI gene expression group's cell-types-analysis package</description>
    <macros>
        <import>garnett_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        garnett_get_std_output.R --input-object '${input_object}' --classifier '${classifier}' --output-file-path '${output_file_path}'
    ]]></command>
    <inputs>
        <param type="data" name="input_object" label="input CDS object" format="rdata" help="CDS object with predicted labels" />
        <param type="data" name="classifier" label="classifier object" format="rdata" help="Classifier object in rdata format" />
    </inputs>
    <outputs>
        <data name="output_file_path" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="input_object" value="cds_pred_labs.rds" />
            <output name="output_file_path" value="garnett_output_tbl.txt" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
        @HELP@

        @VERSION_HISTORY@
    ]]></help>
     <expand macro="citations" />
</tool>