<tool id="garnett_get_feature_genes" name="Garnett - get feature genes" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>Obtain a list of genes used as features in classification model</description>
    <macros>
        <import>garnett_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        garnett_get_feature_genes.R --classifier-object '${classifier_object}'  --database '${database}' --output-path '${output_path}'

        #if $node
        --node '${node}'
        #end if
        #if $convert_ids
        --convert-ids '${convert_ids}'
        #end if
    ]]></command>
    <inputs>
        <param type="data" name="classifier_object" label="classifier object" format="rdata" help="Path to the object of class garnett_classifier, which is either trained via garnett_train_classifier.R or obtained elsewhere" />
        <param type="text" name="node" label="node" value="root" help="In case a hierarchical marker tree was used to train the classifier, specify which node features should be shown. Default is 'root'. For other nodes, use the corresponding parent cell type name" />
        <param type="text" name="database" label="gene database" value="org.Hs.eg.db" help="argument for Bioconductor AnnotationDb-class package used for converting gene IDs" />
        <param type="boolean" name="convert_ids" checked="false" label="convert gene IDs" help="Boolean that indicates whether the gene IDs should be converted into SYMBOL notation" />
    </inputs>
    <outputs>
        <data name="output_path" format="txt" />
    </outputs>
   <help><![CDATA[
        @HELP@

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