| Previous changeset 4:5bf2827cd314 (2020-06-17) Next changeset 6:14eb5128af69 (2020-11-27) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53" |
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modified:
ct_get_empirical_dist.xml |
| b |
| diff -r 5bf2827cd314 -r 36eab91e0ff5 ct_get_empirical_dist.xml --- a/ct_get_empirical_dist.xml Wed Jun 17 12:30:58 2020 -0400 +++ b/ct_get_empirical_dist.xml Mon Jul 13 07:24:39 2020 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="ct_get_empirical_dist" name="Cell types - get empirical distribution" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="ct_get_empirical_dist" name="Cell types - get empirical distribution" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>Get empirical distribution for tool performance table</description> <macros> <import>ct_macros.xml</import> @@ -6,26 +6,31 @@ <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 "${output_list_path}" + get_empirical_dist.R --input-ref-file "${input_ref_file}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}" --num-cores \${GALAXY_SLOTS:-1} --output-path "${output_list_path}" #if $parallel --parallel "${parallel}" #end if + #if $ontology_graph + --ontology-graph "${ontology_graph}" + #end if + #if $tmpdir + --tmpdir "${tmpdir}" + #end if #if $sample_labs --sample-labs "${sample_labs}" #end if #if $exclusions --exclusions "${exclusions}" #end if - #if $sem_sim_metric - --semantic-sim-metric "${sem_sim_metric}" + #if $sem_siml_metric + --semantic-sim-metric "${sem_siml_metric}" #end if + ]]></command> <inputs> <param type="data" name="input_ref_file" label="Input reference file" format="txt" 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="data" name="exclusions" format="yml" label="Exclusions file" optional="true" 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="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" /> <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" /> |