Mercurial > repos > ebi-gxa > ct_get_consensus_outputs
comparison ct_get_consensus_outputs.xml @ 5:87d54692a537 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
author | ebi-gxa |
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date | Mon, 13 Jul 2020 07:24:08 -0400 |
parents | 32101a7373ae |
children | 00abf723fc87 |
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4:32101a7373ae | 5:87d54692a537 |
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1 <tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> | 1 <tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> |
2 <description>Get consensus outputs across multiple tools</description> | 2 <description>Get consensus outputs 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 | |
13 ln -s $'${ontology_graph}' cl-basic.obo; | |
14 | 12 |
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 "${raw_table_output_path}" | 13 get_consensus_output.R --input-dir input_dir --num-cores \${GALAXY_SLOTS:-1} --cl-dictionary "${lab_cl_mapping}" --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}" |
16 #if $tool_table | 14 #if $tool_table |
17 --tool-table "${tool_table}" | 15 --tool-table "${tool_table}" |
18 #end if | 16 #end if |
19 #if $include-sem-siml | 17 #if $ontology_graph |
18 --ontology-graph "${ontology_graph}" | |
19 #end if | |
20 #if $tmpdir | |
21 --tmpdir "${tmpdir}" | |
22 #end if | |
23 #if $include_sem_siml | |
20 --include-sem-siml "${include_sem_siml}" | 24 --include-sem-siml "${include_sem_siml}" |
21 #end if | 25 #end if |
22 #if $parallel | 26 #if $parallel |
23 --parallel "${parallel}" | 27 --parallel "${parallel}" |
24 #end if | 28 #end if |
26 --sort-by-agg-score "${sort_by_agg_score}" | 30 --sort-by-agg-score "${sort_by_agg_score}" |
27 #end if | 31 #end if |
28 #if $exclusions | 32 #if $exclusions |
29 --exclusions "${exclusions}" | 33 --exclusions "${exclusions}" |
30 #end if | 34 #end if |
31 #if $semantic_sim_metric | 35 #if $sem_siml_metric |
32 --semantic-sim-metric "${semantic_sim_metric}" | 36 --semantic-sim-metric "${sem_siml_metric}" |
33 #end if | 37 #end if |
34 ]]></command> | 38 ]]></command> |
35 <inputs> | 39 <inputs> |
36 <param type="data" name="input_tables" label="Aggregated tables" format="txt" multiple="true" help="Aggregated prediction tables from multiple tools" /> | 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="tool_table" format="txt" label="Tools table" help="Table with tools performance metrics" /> | 41 <param type="data" name="tool_table" format="txt" optional="true" label="Tool performance table" help="Table with tools performance metrics" /> |
38 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" /> | 42 <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" /> | 43 <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?" /> | 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?" /> |
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?" /> | 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?" /> |
42 <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" /> | 46 <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" /> |