Mercurial > repos > ebi-gxa > ct_get_consensus_outputs
comparison ct_get_consensus_outputs.xml @ 4:32101a7373ae draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
author | ebi-gxa |
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date | Wed, 17 Jun 2020 12:29:44 -0400 |
parents | 559fbff1f573 |
children | 87d54692a537 |
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3:559fbff1f573 | 4:32101a7373ae |
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14 | 14 |
15 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 "${raw_table_output_path}" | 15 get_consensus_output.R --input-dir input_dir --num-cores \${GALAXY_SLOTS:-1} --cl-dictionary "${lab_cl_mapping}" --ontology-graph cl-basic.obo --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}" |
16 #if $tool_table | 16 #if $tool_table |
17 --tool-table "${tool_table}" | 17 --tool-table "${tool_table}" |
18 #end if | 18 #end if |
19 #if $include-sem-siml | |
20 --include-sem-siml "${include_sem_siml}" | |
21 #end if | |
19 #if $parallel | 22 #if $parallel |
20 --parallel "${parallel}" | 23 --parallel "${parallel}" |
24 #end if | |
25 #if $sort_by_agg_score | |
26 --sort-by-agg-score "${sort_by_agg_score}" | |
21 #end if | 27 #end if |
22 #if $exclusions | 28 #if $exclusions |
23 --exclusions "${exclusions}" | 29 --exclusions "${exclusions}" |
24 #end if | 30 #end if |
25 #if $semantic_sim_metric | 31 #if $semantic_sim_metric |
28 ]]></command> | 34 ]]></command> |
29 <inputs> | 35 <inputs> |
30 <param type="data" name="input_tables" label="Aggregated tables" format="txt" multiple="true" help="Aggregated prediction tables from multiple tools" /> | 36 <param type="data" name="input_tables" label="Aggregated tables" format="txt" multiple="true" help="Aggregated prediction tables from multiple tools" /> |
31 <param type="data" name="tool_table" format="txt" label="Tools table" help="Table with tools performance metrics" /> | 37 <param type="data" name="tool_table" format="txt" label="Tools table" help="Table with tools performance metrics" /> |
32 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" /> | 38 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" /> |
39 <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" /> | |
40 <param type="boolean" name="include_sem_siml" label="Include Semantic Similarity" checked="false" help="Should semantic similarity be included in calculation of combined score?" /> | |
41 <param type="boolean" name="sort_by_agg_score" label="Sort by aggregated score" checked="true" help="Should the cells be ordered by aggregated score?" /> | |
33 <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" /> | 42 <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" /> |
34 <param type="data" name="lab_cl_mapping" format="rdata" label="cl terms mapping" help="Label - CL term mapping" /> | 43 <param type="data" name="lab_cl_mapping" format="rdata" label="cl terms mapping" help="Label - CL term mapping" /> |
35 <param type="data" name="ontology_graph" format="obo" label="Ontology graph" help="Ontology graph to run similairty calculations" /> | 44 <param type="data" name="ontology_graph" format="obo" label="Ontology graph" optional="true" help="Ontology graph to run similairty calculations" /> |
36 <param type="text" name="semantic_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" /> | 45 <expand macro="sem_siml_options" /> |
37 </inputs> | 46 </inputs> |
38 <outputs> | 47 <outputs> |
39 <data name="summary_table_output_path" format="txt" /> | 48 <data name="summary_table_output_path" format="txt" /> |
40 <data name="raw_table_output_path" format="txt" /> | 49 <data name="raw_table_output_path" format="txt" /> |
41 </outputs> | 50 </outputs> |