<tool id="update_marker_file" name="Garnett - update markers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>Update marker file by filtering out suboptimal markers</description>
   <macros>
        <import>garnett_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        update_marker_file.R --marker-list-obj '${marker_list_obj}' --marker-check-file '${marker_check_file}'    --updated-marker-file '${updated_marker_file}'

        #if $summary_col
        --summary-col '${summary_col}'
        #end if
        #if $cell_type_col
        --cell-type-col '${cell_type_col}'
        #end if
        #if $gene_id_col
        --gene-id-col '${gene_id_col}'
        #end if
    ]]></command>
    <inputs>
        <param type="data" name="marker_list_obj" label="Marker list object" format="rdata" help="Serialised object containing markers list produced by garnett_transform_markers" />
        <param type="data" name="marker_check_file" label="marker check file" format="txt" help="Path to the file with marker gene assessment done by garnett" />
        <param type="text" name="summary_col" value="summary" label="Name of summary column" help="Marker gene assessment column name" />
        <param type="text" name="cell_type_col" value="cell_type" label="Name of cell type column" help="Marker gene assessment column name" />
        <param type="text" name="gene_id_col" value="gene_id" label="Name of gene id column" help="Gene id column name in marker assessment file" />
    </inputs>
    <outputs>
        <data name="updated_marker_file" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="marker_list_obj" value="marker_list.rds" />
            <param name="marker_check_file" value="marker_check.txt" />
            <output name="updated_marker_file" file="markers_upd.txt" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
        @HELP@

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