Mercurial > repos > ebi-gxa > ct_get_tool_perf_table
changeset 2:fba1a5c44387 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
author | ebi-gxa |
---|---|
date | Fri, 24 Apr 2020 15:08:31 +0000 |
parents | 1199f05e9d24 |
children | bd7cfdc6e635 |
files | ct_get_tool_perf_table.xml |
diffstat | 1 files changed, 26 insertions(+), 2 deletions(-) [+] |
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--- a/ct_get_tool_perf_table.xml Thu Apr 16 08:47:59 2020 +0000 +++ b/ct_get_tool_perf_table.xml Fri Apr 24 15:08:31 2020 +0000 @@ -12,12 +12,36 @@ ln -s $'${ontology_graph}' cl-basic.obo; - get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --num-cores "${num_cores}" --exclusions "${exclusions}" --parallel "${parallel}" --ontology-graph cl-basic.obo --lab-cl-mapping "${lab_cl_mapping}" --barcode-col-ref "${barcode_col_ref}" --barcode-col-pred "${barcode_col_pred}" --label-column-ref "${label_col_ref}" --label-column-pred "${label_col_pred}" --semantic-sim-metric "${semantic_sim_metric}" --output-path "${output_path}" ]]></command> + get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --num-cores \${GALAXY_SLOTS:-1} --ontology-graph cl-basic.obo --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}" + + #if $exclusions + --exclusions "${exclusions}" + #end if + #if $parallel + --parallel "${parallel}" + #end if + #if $barcode_col_ref + --barcode-col-ref "${barcode_col_ref}" + #end if + #if $barcode_col_pred + --barcode-col-pred "${barcode_col_pred}" + #end if + #if $label_col_ref + --label-column-ref "${label_col_ref}" + #end if + #if $label_col_pred + --label-column-pred "${label_col_pred}" + #end if + #if $semantic_sim_metric + --semantic-sim-metric "${semantic_sim_metric}" + #end if + + + ]]></command> <inputs> <param type="data" name="input_files" label="Input tables" multiple="true" format="txt" help="Classification tables obtained from multiple classisifiers" /> <param type="data" name="ref_file" label="Reference metadata file" format="txt" help="Metadata file with reference labels" /> <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" label="Number of cores" value='1' help="Number of cores used for computation" /> <param type="data" name="exclusions" label="Exclusions" format="yml" optional="true" help="Config file with exclusions" /> <param type="data" name="ontology_graph" label="Ontology graph" format="obo" help="Ontology graph to run semantis similarity computations" /> <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" />