comparison ct_get_consensus_outputs.xml @ 7:0917f5e09d83 draft default tip

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"

6:00abf723fc87

<tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy3" 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
        
        get_consensus_output.R --input-dir input_dir --num-cores \${GALAXY_SLOTS:-1} --cl-dictionary "${lab_cl_mapping}"   --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}"
        #if $tool_table
        --tool-table "${tool_table}"
        #end if
        #if $ontology_graph
        --ontology-graph "${ontology_graph}"
        #end if
        #if $tmpdir
        --tmpdir "${tmpdir}"
        #end if
        #if $include_sem_siml
        --include-sem-siml "${include_sem_siml}"
        #end if
        #if $parallel
        --parallel "${parallel}"
        #end if
        #if $sort_by_agg_score
        --sort-by-agg-score "${sort_by_agg_score}"
        #end if
        #if $exclusions
        --exclusions "${exclusions}"
        #end if
        #if $sem_siml_metric
        --semantic-sim-metric "${sem_siml_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" optional="true" label="Tool performance 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="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" />
        <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="boolean" name="sort_by_agg_score" label="Sort by aggregated score" checked="true" help="Should the cells be ordered by aggregated score?" />
        <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" optional="true" help="Ontology graph to run similairty calculations" />
        <expand macro="sem_siml_options" />
    </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[

7:0917f5e09d83

<tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>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
        
        get_consensus_output.R --input-dir input_dir --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --cl-dictionary "${lab_cl_mapping}"   --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}" --tmpdir ./
        #if $tool_table
        --tool-table "${tool_table}"
        #end if
        #if $ontology_graph
        --ontology-graph "${ontology_graph}"
        #end if
        #if $include_sem_siml
        --include-sem-siml "${include_sem_siml}"
        #end if
        #if $sort_by_agg_score
        --sort-by-agg-score "${sort_by_agg_score}"
        #end if
        #if $exclusions
        --exclusions "${exclusions}"
        #end if
        #if $sem_siml_metric
        --semantic-sim-metric "${sem_siml_metric}" 
        #end if
        #if $true_labels
        --true-labels "${true_labels}" 
        #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" optional="true" label="Tool performance table" help="Table with tools performance metrics" />
        <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="boolean" name="sort_by_agg_score" label="Sort by aggregated score" checked="true" help="Should the cells be ordered by aggregated score?" />
        <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" optional="true" help="Ontology graph to run similairty calculations" />
        <param type="data" name="true_labels" format="txt" optional="true" label="True Labels" help="Path to the true labels tsv file in case tool performance is evaluated. Expected columns: cell_id, true_label, ontology_term" />
        <expand macro="sem_siml_options" />
    </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-cell.txt,prod_combined_tools/scmap-cluster.txt,prod_combined_tools/scpred.txt" />
            <param name="tool_table" value="tool_perf_pvals.tsv" />
            <param name="exclusions" value="exclusions.yml" />
            <param name="lab_cl_mapping" value="label_cl_dict.rds" />
            <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[