comparison ct_get_consensus_outputs.xml @ 5:87d54692a537 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"

4:32101a7373ae

<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 $include-sem-siml
        --include-sem-siml "${include_sem_siml}"
        #end if
        #if $parallel
        --parallel "${parallel}"
        #end if

        --sort-by-agg-score "${sort_by_agg_score}"
        #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="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" />

5:87d54692a537

<tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy2" 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

        --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" />