Mercurial > repos > ebi-gxa > ct_get_consensus_outputs

comparison ct_get_consensus_outputs.xml @ 0:66cdd8438ac6 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
author ebi-gxa
date Wed, 08 Apr 2020 11:34:17 -0400
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-1:000000000000 0:66cdd8438ac6
1 <tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>Get consensus outputs across multiple tools</description>
3 <macros>
4 <import>ct_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p input_dir;
9 #for $table in $input_tables:
10 cp '$table' input_dir/;
11 #end for
12
13 ln -s $'${ontology_graph}' cl-basic.obo;
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>
16 <inputs>
17 <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" />
19 <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" />
22 <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" />
24 <param type="text" name="semantic_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" />
25 </inputs>
26 <outputs>
27 <data name="summary_table_output_path" format="txt" />
28 <data name="raw_table_output_path" format="txt" />
29 </outputs>
30 <tests>
31 <test>
32 <param name="input_tables" value="prod_combined_tools/scmap_combined.tsv,prod_combined_tools/scpred_combined.tsv" />
33 <param name="tool_table" value="tool_perf_pvals.tsv" />
34 <param name="exclusions" value="exclusions.yml" />
35 <param name="parallel" value="TRUE" />
36 <param name="lab_cl_mapping" value="label_cl_dict.rds" />
37 <param name="ontology_graph" value="cl-basic.obo" />
38 <output name="summary_table_output_path" file="summary_output_table.tsv" compare="sim_size" />
39 <output name="raw_table_output_path" file="raw_labels_table.tsv" compare="sim_size" />
40 </test>
41 </tests>
42 <help><![CDATA[
43 @HELP@
44
45 @VERSION_HISTORY@
46 ]]></help>
47 <expand macro="citations" />
48 </tool>