<tool id="garnett_transform_markers" name="Garnett - transform markes" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>Transform marker files from Single Cell Expression Atlas format to that compatible with Garnett</description>
    <macros>
        <import>garnett_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        transform_marker_file.R --input-marker-file '${input_marker_file}' --marker-list '${marker_list}'  --garnett-marker-file '${garnett_marker_file}'

        #if $pval_col
        --pval-col '${pval_col}'
        #end if
        #if $pval_threshold
        --pval-threshold '${pval_threshold}'
        #end if
        #if $groups_col
        --groups-col '${groups_col}'
        #end if
        #if $gene_names
        --gene-names '${gene_names}'
        #end if
    ]]></command>
    <inputs>
        <param type="data" name="input_marker_file" format="txt" label="Input marker file" help="Path to the SCXA-style marker gene file in .txt format" />
        <param type="text" name="pval_col" value="pvals" label="p-value column name" help="Column name of marker p-values" />
        <param type="float" name="pval_threshold" value="0.05" label="p-value threshold" help="Cut-off p-value for marker genes" />
        <param type="text" name="groups_col" value="groups" label="groups column" help="Column name of cell groups (i.e. cluster IDs or cell types) in marker file" />
        <param type="text" name="gene_names" value="names" label="gene names" help="Column containing gene names in marker file" />
    </inputs>
    <outputs>
        <data name="garnett_marker_file" format="txt" />
        <data name="marker_list" format="rdata" />
    </outputs>
    <tests>
        <test>
            <param name="input_marker_file" value="ref_marker_genes.txt" />
            <param name="marker_list" value="marker_list.rds" />
            <output name="garnett_marker_file" file="markers_transformed.txt" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
         @HELP@

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