Mercurial > repos > ebi-gxa > ct_get_consensus_outputs

comparison ct_get_consensus_outputs.xml @ 7:0917f5e09d83 draft default tip

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:38:17 +0000
parents 00abf723fc87
children
comparison
equal deleted inserted replaced
6:00abf723fc87 7:0917f5e09d83
1 <tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@"> 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> 2 <description>across multiple tools</description>
3 <macros> 3 <macros>
4 <import>ct_macros.xml</import> 4 <import>ct_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p input_dir; 8 mkdir -p input_dir;
9 #for $table in $input_tables: 9 #for $table in $input_tables:
10 cp '$table' input_dir/; 10 cp '$table' input_dir/;
11 #end for 11 #end for
12 12
13 get_consensus_output.R --input-dir input_dir --num-cores \${GALAXY_SLOTS:-1} --cl-dictionary "${lab_cl_mapping}" --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}" 13 get_consensus_output.R --input-dir input_dir --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --cl-dictionary "${lab_cl_mapping}" --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}" --tmpdir ./
14 #if $tool_table 14 #if $tool_table
15 --tool-table "${tool_table}" 15 --tool-table "${tool_table}"
16 #end if 16 #end if
17 #if $ontology_graph 17 #if $ontology_graph
18 --ontology-graph "${ontology_graph}" 18 --ontology-graph "${ontology_graph}"
19 #end if 19 #end if
20 #if $tmpdir
21 --tmpdir "${tmpdir}"
22 #end if
23 #if $include_sem_siml 20 #if $include_sem_siml
24 --include-sem-siml "${include_sem_siml}" 21 --include-sem-siml "${include_sem_siml}"
25 #end if
26 #if $parallel
27 --parallel "${parallel}"
28 #end if 22 #end if
29 #if $sort_by_agg_score 23 #if $sort_by_agg_score
30 --sort-by-agg-score "${sort_by_agg_score}" 24 --sort-by-agg-score "${sort_by_agg_score}"
31 #end if 25 #end if
32 #if $exclusions 26 #if $exclusions
33 --exclusions "${exclusions}" 27 --exclusions "${exclusions}"
34 #end if 28 #end if
35 #if $sem_siml_metric 29 #if $sem_siml_metric
36 --semantic-sim-metric "${sem_siml_metric}" 30 --semantic-sim-metric "${sem_siml_metric}"
37 #end if 31 #end if
32 #if $true_labels
33 --true-labels "${true_labels}"
34 #end if
38 ]]></command> 35 ]]></command>
39 <inputs> 36 <inputs>
40 <param type="data" name="input_tables" label="Aggregated tables" format="txt" multiple="true" help="Aggregated prediction tables from multiple tools" /> 37 <param type="data" name="input_tables" label="Aggregated tables" format="txt" multiple="true" help="Aggregated prediction tables from multiple tools" />
41 <param type="data" name="tool_table" format="txt" optional="true" label="Tool performance table" help="Table with tools performance metrics" /> 38 <param type="data" name="tool_table" format="txt" optional="true" label="Tool performance table" help="Table with tools performance metrics" />
42 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
43 <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" />
44 <param type="boolean" name="include_sem_siml" label="Include Semantic Similarity" checked="false" help="Should semantic similarity be included in calculation of combined score?" /> 39 <param type="boolean" name="include_sem_siml" label="Include Semantic Similarity" checked="false" help="Should semantic similarity be included in calculation of combined score?" />
45 <param type="boolean" name="sort_by_agg_score" label="Sort by aggregated score" checked="true" help="Should the cells be ordered by aggregated score?" /> 40 <param type="boolean" name="sort_by_agg_score" label="Sort by aggregated score" checked="true" help="Should the cells be ordered by aggregated score?" />
46 <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" /> 41 <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" />
47 <param type="data" name="lab_cl_mapping" format="rdata" label="cl terms mapping" help="Label - CL term mapping" /> 42 <param type="data" name="lab_cl_mapping" format="rdata" label="cl terms mapping" help="Label - CL term mapping" />
48 <param type="data" name="ontology_graph" format="obo" label="Ontology graph" optional="true" help="Ontology graph to run similairty calculations" /> 43 <param type="data" name="ontology_graph" format="obo" label="Ontology graph" optional="true" help="Ontology graph to run similairty calculations" />
44 <param type="data" name="true_labels" format="txt" optional="true" label="True Labels" help="Path to the true labels tsv file in case tool performance is evaluated. Expected columns: cell_id, true_label, ontology_term" />
49 <expand macro="sem_siml_options" /> 45 <expand macro="sem_siml_options" />
50 </inputs> 46 </inputs>
51 <outputs> 47 <outputs>
52 <data name="summary_table_output_path" format="txt" /> 48 <data name="summary_table_output_path" format="txt" />
53 <data name="raw_table_output_path" format="txt" /> 49 <data name="raw_table_output_path" format="txt" />
54 </outputs> 50 </outputs>
55 <tests> 51 <tests>
56 <test> 52 <test>
57 <param name="input_tables" value="prod_combined_tools/scmap_combined.tsv,prod_combined_tools/scpred_combined.tsv" /> 53 <param name="input_tables" value="prod_combined_tools/scmap-cell.txt,prod_combined_tools/scmap-cluster.txt,prod_combined_tools/scpred.txt" />
58 <param name="tool_table" value="tool_perf_pvals.tsv" /> 54 <param name="tool_table" value="tool_perf_pvals.tsv" />
59 <param name="exclusions" value="exclusions.yml" /> 55 <param name="exclusions" value="exclusions.yml" />
60 <param name="parallel" value="TRUE" />
61 <param name="lab_cl_mapping" value="label_cl_dict.rds" /> 56 <param name="lab_cl_mapping" value="label_cl_dict.rds" />
62 <param name="ontology_graph" value="cl-basic.obo" />
63 <output name="summary_table_output_path" file="summary_output_table.tsv" compare="sim_size" /> 57 <output name="summary_table_output_path" file="summary_output_table.tsv" compare="sim_size" />
64 <output name="raw_table_output_path" file="raw_labels_table.tsv" compare="sim_size" /> 58 <output name="raw_table_output_path" file="raw_labels_table.tsv" compare="sim_size" />
65 </test> 59 </test>
66 </tests> 60 </tests>
67 <help><![CDATA[ 61 <help><![CDATA[