annotate ct_get_empirical_dist.xml @ 4:5bf2827cd314 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"

<tool id="ct_get_empirical_dist" name="Cell types - get empirical distribution" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>Get empirical distribution for tool performance table</description>
    <macros>
        <import>ct_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        ln -s $'${ontology_graph}' cl-basic.obo;

        get_empirical_dist.R --input-ref-file "${input_ref_file}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}" --num-cores \${GALAXY_SLOTS:-1} --ontology-graph cl-basic.obo --output-path "${output_list_path}" 

        #if $parallel
        --parallel "${parallel}"
        #end if
        #if $sample_labs
        --sample-labs "${sample_labs}"
        #end if
        #if $exclusions
        --exclusions "${exclusions}"
        #end if
        #if $sem_sim_metric
        --semantic-sim-metric "${sem_sim_metric}"
        #end if
        ]]></command>
    <inputs>
        <param type="data" name="input_ref_file" label="Input reference file" format="txt" help="Text file with reference cell labels" />
        <param type="data" name="exclusions" format="yml" label="Exclusions file" help="YML file with excluded/unlabelled terms" />
        <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" />
        <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="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
        <param type="integer" name="num_iter" value='5' label="Number of iterations" help="Number of simulations to generate empirical CDF" />
        <param type="integer" name="sample_labs" value='50' label="Number of labels to sample" help="Numbre of labels to sample for each permutation" />
        <param type="data" name="ontology_graph" label="Ontology graph" format="obo" optional="true" help="Ontology graph to run semantis similarity computations" />
        <expand macro="sem_siml_options" />
    </inputs>
    <outputs>
        <data name="output_list_path" format="rdata" />
    </outputs>
    <tests>
        <test>
            <param name="input_ref_file" value="reference_sdrf.tsv" />
            <param name="label_col_ref" value="Sample.Characteristic.cell.type." />
            <param name="ontology_graph" value="cl-basic.obo" />
            <param name="exclusions" value="exclusions.yml" />
            <param name="parallel" value="TRUE" />
            <param name="lab_cl_mapping" value="label_cl_dict.rds" />
            <output name="output_list_path" file="empirical_dist_list.rds" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
    @HELP@

    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>