<tool id="ct_get_tool_perf_table" name="Cell types - get tool performance table" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>Get performance table for a list of outputs generated by various tools</description>
    <macros>
         <import>ct_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p input_dir;
        #for $input_file in $input_files:
          cp '$input_file' input_dir/;
        #end for

        ln -s $'${ontology_graph}' cl-basic.obo;
       
        get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --num-cores \${GALAXY_SLOTS:-1}   --ontology-graph cl-basic.obo --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}"

        #if $exclusions
        --exclusions "${exclusions}"
        #end if
        #if $parallel
        --parallel "${parallel}"
        #end if
        #if $include_sem_siml
        --include-sem-siml "${include_sem_siml}"
        #end if
        #if $barcode_col_ref
        --barcode-col-ref "${barcode_col_ref}"
        #end if
        #if $barcode_col_pred
        --barcode-col-pred "${barcode_col_pred}"
        #end if
        #if $label_col_ref
        --label-column-ref "${label_col_ref}" 
        #end if
        #if $label_col_pred
        --label-column-pred "${label_col_pred}" 
        #end if
        #if $semantic_sim_metric
        --semantic-sim-metric "${semantic_sim_metric}" 
        #end if

         ]]></command>
    <inputs>
        <param type="data" name="input_files" label="Input tables" multiple="true" format="txt" help="Classification tables obtained from multiple classisifiers" />
        <param type="data" name="ref_file" label="Reference metadata file" format="txt" help="Metadata file with reference labels" />
        <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
        <param type="boolean" name="include_sem_siml" label="Include Semantic Similarity" checked="false" help="Should semantic similarity be included in calculation of combined score?" />
        <param type="data" name="exclusions" label="Exclusions" format="yml" optional="true" help="Config file with exclusions" />
        <param type="data" name="ontology_graph" label="Ontology graph" optional="true" format="obo" help="Ontology graph to run semantis similarity computations" />
        <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" />
        <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" />
        <param type="text" name="barcode_col_ref" label="Reference file barcode field" value='cell_id' help="Name of barcode field in reference metadata file" />
        <param type="text" name="barcode_col_pred" label="Predicted file barcode field" value="cell_id" help="Name of barcode field in predictions file" />
        <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" />
        <param type="text" name="label_col_pred" label="Predicted file label column" value="pred_label" help="Name of label field in predictions file" />
        <expand macro="sem_siml_options" />
    </inputs>
    <outputs>
         <data name="output_path" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="input_files" value="results_dir/garnett_output.txt,results_dir/scmap-cell_output.txt,results_dir/scmap-cluster_output.txt,results_dir/scpred_output.txt" />
            <param name="ref_file" value="reference_sdrf.tsv" />
            <param name="ontology_graph" value="cl-basic.obo" />
            <param name="lab_cl_mapping" value="label_cl_dict.rds" />
            <param name="parallel" value="TRUE" />
            <param name="exclusions" value="exclusions.yml" />
            <param name="barcode_col_ref" value="Assay" />
            <param name="barcode_col_pred" value="cell_id" />
            <param name="label_col_ref" value="Sample.Characteristic.cell.type." />
            <param name="label_col_pred" value="predicted_label" />
            <output name="output_path" file="tool_perf_table.tsv" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>