| Previous changeset 0:196cc72cebd1 (2020-04-08) Next changeset 2:25bb7e49e10d (2020-04-27) |
|
Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed" |
|
modified:
ct_get_empirical_dist.xml ct_macros.xml |
| b |
| diff -r 196cc72cebd1 -r 9d5e6a4ec5b5 ct_get_empirical_dist.xml --- a/ct_get_empirical_dist.xml Wed Apr 08 11:34:54 2020 -0400 +++ b/ct_get_empirical_dist.xml Fri Apr 24 11:20:00 2020 -0400 |
| [ |
| @@ -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> |
| b |
| diff -r 196cc72cebd1 -r 9d5e6a4ec5b5 ct_macros.xml --- a/ct_macros.xml Wed Apr 08 11:34:54 2020 -0400 +++ b/ct_macros.xml Fri Apr 24 11:20:00 2020 -0400 |
| b |
| @@ -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> |