<tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>Get consensus outputs across multiple tools</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

        ln -s $'${ontology_graph}' cl-basic.obo;
        
        get_consensus_output.R --input-dir input_dir --num-cores \${GALAXY_SLOTS:-1} --cl-dictionary "${lab_cl_mapping}"  --ontology-graph cl-basic.obo --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}"
        #if $tool_table
        --tool-table "${tool_table}"
        #end if
        #if $parallel
        --parallel "${parallel}"
        #end if
        #if $exclusions
        --exclusions "${exclusions}"
        #end if
        #if $semantic_sim_metric
        --semantic-sim-metric "${semantic_sim_metric}" 
        #end if
         ]]></command>
    <inputs>
        <param type="data" name="input_tables" label="Aggregated tables" format="txt" multiple="true" help="Aggregated prediction tables from multiple tools" />
        <param type="data" name="tool_table" format="txt" label="Tools table" help="Table with tools performance metrics" />
        <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
        <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" />
        <param type="data" name="lab_cl_mapping" format="rdata" label="cl terms mapping" help="Label - CL term mapping" />
        <param type="data" name="ontology_graph" format="obo" label="Ontology graph" help="Ontology graph to run similairty calculations" />
        <param type="text" name="semantic_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" />
    </inputs>
    <outputs>
        <data name="summary_table_output_path" format="txt" />
        <data name="raw_table_output_path" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="input_tables" value="prod_combined_tools/scmap_combined.tsv,prod_combined_tools/scpred_combined.tsv" />
            <param name="tool_table" value="tool_perf_pvals.tsv" />
            <param name="exclusions" value="exclusions.yml" />
            <param name="parallel" value="TRUE" />
            <param name="lab_cl_mapping" value="label_cl_dict.rds" />
            <param name="ontology_graph" value="cl-basic.obo" />
            <output name="summary_table_output_path" file="summary_output_table.tsv" compare="sim_size" />
            <output name="raw_table_output_path" file="raw_labels_table.tsv" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>