<tool id="ct_combine_tool_outputs" name="Cell types - combine tools outputs" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>Combine predictions for single tool from multiple datasets</description>
    <macros>
        <import>ct_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p input_dir;
        #for $table in $input_tables:
          cp '$table' input_dir/;
        #end for

        combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --scores "${scores}" --output-table "${output_table}" 

        #if $exclusions
        --exclusions "${exclusions}"
        #end if
        ]]></command>
    <inputs>
        <param type="data" name="input_tables" label="Tables with predicted labels" multiple="true" format="txt" help="Standardised tables obtained from multiple classifiers" />
        <param type="integer" name="top_labels_num" label="Number of top labels" value='3' help="Number of top labels to select" />
        <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" />
        <param type="boolean" name="scores" label="scores" checked="false" help="Are scores included into the tool outpus?" />
    </inputs>
    <outputs>
        <data name="output_table" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="input_tables" value="prod_outputs_scpred/E-MTAB-6386_scpred_final-labs.tsv,prod_outputs_scpred/OTHER-DATASET_scpred_final-labs.tsv" />
            <param name="scores" value="TRUE" />
            <param name="exclusions" value="exclusions.yml" />
            <output name="output_table" file="combined_results.tsv" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>