Mercurial > repos > ebi-gxa > ct_get_consensus_outputs

comparison ct_get_consensus_outputs.xml @ 1:a31bc9849f91 draft

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"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 11:19:28 -0400
parents 66cdd8438ac6
children 94927cc336ba
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0:66cdd8438ac6 1:a31bc9849f91
10 cp '$table' input_dir/; 10 cp '$table' input_dir/;
11 #end for 11 #end for
12 12
13 ln -s $'${ontology_graph}' cl-basic.obo; 13 ln -s $'${ontology_graph}' cl-basic.obo;
14 14
15 get_consensus_output.R --input-dir input_dir --tool-table "${tool_table}" --num-cores "${num_cores}" --cl-dictionary "${lab_cl_mapping}" --parallel "${parallel}" --exclusions "${exclusions}" --ontology-graph cl-basic.obo --semantic-sim-metric "${semantic_sim_metric}" --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}" ]]></command> 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 $tool_table
17 --tool-table "${tool_table}"
18 #end if
19 #if $parallel
20 --parallel "${parallel}"
21 #end if
22 #if $exclusions
23 --exclusions "${exclusions}"
24 #end if
25 #if $semantic_sim_metric
26 --semantic-sim-metric "${semantic_sim_metric}"
27 #end if
28 ]]></command>
16 <inputs> 29 <inputs>
17 <param type="data" name="input_tables" label="Aggregated tables" format="tsv" multiple="true" help="Aggregated prediction tables from multiple tools" /> 30 <param type="data" name="input_tables" label="Aggregated tables" format="tsv" multiple="true" help="Aggregated prediction tables from multiple tools" />
18 <param type="data" name="tool_table" format="tsv" label="Tools table" help="Table with tools performance metrics" /> 31 <param type="data" name="tool_table" format="tsv" label="Tools table" help="Table with tools performance metrics" />
19 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" /> 32 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
20 <param type="integer" name="num_cores" value='4' label="Number of cores" help="Number of cores to run the process" />
21 <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" /> 33 <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" />
22 <param type="data" name="lab_cl_mapping" format="rdata" label="cl terms mapping" help="Label - CL term mapping" /> 34 <param type="data" name="lab_cl_mapping" format="rdata" label="cl terms mapping" help="Label - CL term mapping" />
23 <param type="data" name="ontology_graph" format="obo" label="Ontology graph" help="Ontology graph to run similairty calculations" /> 35 <param type="data" name="ontology_graph" format="obo" label="Ontology graph" help="Ontology graph to run similairty calculations" />
24 <param type="text" name="semantic_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" /> 36 <param type="text" name="semantic_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" />
25 </inputs> 37 </inputs>