| Previous changeset 0:66cdd8438ac6 (2020-04-08) Next changeset 2:94927cc336ba (2020-04-27) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed" |
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modified:
ct_get_consensus_outputs.xml ct_macros.xml |
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| diff -r 66cdd8438ac6 -r a31bc9849f91 ct_get_consensus_outputs.xml --- a/ct_get_consensus_outputs.xml Wed Apr 08 11:34:17 2020 -0400 +++ b/ct_get_consensus_outputs.xml Fri Apr 24 11:19:28 2020 -0400 |
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| @@ -12,12 +12,24 @@ ln -s $'${ontology_graph}' cl-basic.obo; - get_consensus_output.R --input-dir input_dir --tool-table "${tool_table}" --num-cores "${num_cores}" --cl-dictionary "${lab_cl_mapping}" --parallel "${parallel}" --exclusions "${exclusions}" --ontology-graph cl-basic.obo --semantic-sim-metric "${semantic_sim_metric}" --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}" ]]></command> + 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 $parallel + --parallel "${parallel}" + #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="tsv" multiple="true" help="Aggregated prediction tables from multiple tools" /> <param type="data" name="tool_table" format="tsv" 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="integer" name="num_cores" value='4' label="Number of cores" help="Number of cores to run the process" /> <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" help="Ontology graph to run similairty calculations" /> |
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| diff -r 66cdd8438ac6 -r a31bc9849f91 ct_macros.xml --- a/ct_macros.xml Wed Apr 08 11:34:17 2020 -0400 +++ b/ct_macros.xml Fri Apr 24 11:19:28 2020 -0400 |
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| @@ -29,7 +29,8 @@ url = {https://github.com/ebi-gene-expression-group/cell-types-analysis.git}, } </citation> + <citation type="doi">10.1101/2020.04.08.032698</citation> <yield /> </citations> </xml> -</macros> \ No newline at end of file +</macros> |