<tool id="ct_build_cell_ontology_dict" name="Cell types - build cell ontology map" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>Create a mapping from labels to CL terms</description>
    <macros>
        <import>ct_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p input_dir;
        #for $sdrf in $input_sdrfs:
            cp '$sdrf' input_dir/;
        #end for

        build_cell_ontology_dict.R --input-dir input_dir  --output-dict-path "${output_dict_path}" --output-text-path "${output_txt_path}"
        #if $condensed_sdrf
        --condensed-sdrf "${condensed_sdrf}" 
        #end if
        #if $barcode_col_name
        --barcode-col-name "${barcode_col_name}"
        #end if
        #if $cell_label_col_name
        --cell-label-col-name "${cell_label_col_name}"
        #end if
        #if $cell_ontology_col_name
        --cell-ontology-col-name "${cell_ontology_col_name}" 
        #end if
         ]]></command>
    <inputs>
        <param type="data" name="input_sdrfs" label="Input SDRF tables" multiple="true" format="txt" help="Input SDRF tables" />
        <param type="boolean" name="condensed_sdrf" checked="false" label="Condensed SDRF" help="Are the supplied SDRFs of condensed format?" />
        <param type="text" name="barcode_col_name" label="Barcode column name" value="id" help="Name of the barcode field in provided SDRF files" />
        <param type="text" name="cell_label_col_name" label="Cell label column name" value="cell.type" help="Name of the cell label field name in provided SDRF files" />
        <param type="text" name="cell_ontology_col_name" label="Cell ontology column name" value="cell.type.ontology" help="Name of the cell ontology terms column in SDRF files (must be identical across all files)" />
    </inputs>
    <outputs>
        <data name="output_dict_path" format="rdata" />
        <data name="output_txt_path" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="input_sdrfs" value="SDRFs/ref_condensed_sdrf.tsv,SDRFs/ref_condensed_sdrf_1.tsv" />
            <param name="condensed_sdrf" value="TRUE" />
            <output name="output_dict_path" file="label_cl_dict.rds" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>