Mercurial > repos > ebi-gxa > ct_get_empirical_dist
changeset 2:1758678269cb 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 15:08:02 +0000 |
parents | 1d8cb691d37c |
children | 6fc67b8caa21 |
files | ct_get_empirical_dist.xml |
diffstat | 1 files changed, 13 insertions(+), 3 deletions(-) [+] |
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--- a/ct_get_empirical_dist.xml Thu Apr 16 08:47:34 2020 +0000 +++ b/ct_get_empirical_dist.xml Fri Apr 24 15:08:02 2020 +0000 @@ -6,9 +6,20 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - ln -s $'${ontology_graph}' cl-basic.obo; + 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 "${output_list_path}" - get_empirical_dist.R --input-ref-file "${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> + #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" /> @@ -16,7 +27,6 @@ <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>