comparison ct_get_empirical_dist.xml @ 1:9d5e6a4ec5b5 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

0:196cc72cebd1

        <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 "${input_ref_file}" --parallel "${parallel}" --exclusions "${exclusions}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}" --num-cores "${num_cores}" --ontology-graph cl-basic.obo --semantic-sim-metric "${sem_sim_metric}" --output-path "${output_list_path}" ]]></command>
    <inputs>
        <param type="data" name="input_ref_file" label="Input reference file" format="tsv" 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="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="num_cores" value='4' label="Number of cores" help="Number of cores to run the process" />
        <param type="data" name="ontology_graph" label="Ontology graph" format="obo" help="Ontology graph to run semantis similarity computations" />
        <param type="text" name="sem_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" />
    </inputs>
    <outputs>
        <data name="output_list_path" format="rdata" />

1:9d5e6a4ec5b5

        <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 $exclusions
        --exclusions "${exclusions}"
        #end if
        #if $exclusions
        --semantic-sim-metric "${sem_sim_metric}"
        #end if
        ]]></command>
    <inputs>
        <param type="data" name="input_ref_file" label="Input reference file" format="tsv" 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="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="data" name="ontology_graph" label="Ontology graph" format="obo" help="Ontology graph to run semantis similarity computations" />
        <param type="text" name="sem_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" />
    </inputs>
    <outputs>
        <data name="output_list_path" format="rdata" />