Mercurial > repos > ebi-gxa > ct_get_consensus_outputs

comparison ct_get_consensus_outputs.xml @ 4:32101a7373ae draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
author ebi-gxa
date Wed, 17 Jun 2020 12:29:44 -0400
parents 559fbff1f573
children 87d54692a537
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3:559fbff1f573 4:32101a7373ae
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>