Mercurial > repos > ebi-gxa > ct_get_consensus_outputs

annotate ct_get_consensus_outputs.xml @ 5:87d54692a537 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
author ebi-gxa
date Mon, 13 Jul 2020 07:24:08 -0400
parents 32101a7373ae
children 00abf723fc87
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
87d54692a537 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
ebi-gxa
parents: 4
diff changeset
1 <tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
0
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
2 <description>Get consensus outputs across multiple tools</description>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
3 <macros>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
4 <import>ct_macros.xml</import>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
5 </macros>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
6 <expand macro="requirements" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
8 mkdir -p input_dir;
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
9 #for $table in $input_tables:
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
10 cp '$table' input_dir/;
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
11 #end for
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
12
5
87d54692a537 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
ebi-gxa
parents: 4
diff changeset
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}"
1
a31bc9849f91 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
14 #if $tool_table
a31bc9849f91 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
15 --tool-table "${tool_table}"
a31bc9849f91 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
16 #end if
5
87d54692a537 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
ebi-gxa
parents: 4
diff changeset
17 #if $ontology_graph
87d54692a537 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
ebi-gxa
parents: 4
diff changeset
18 --ontology-graph "${ontology_graph}"
87d54692a537 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
ebi-gxa
parents: 4
diff changeset
19 #end if
87d54692a537 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
ebi-gxa
parents: 4
diff changeset
20 #if $tmpdir
87d54692a537 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
ebi-gxa
parents: 4
diff changeset
21 --tmpdir "${tmpdir}"
87d54692a537 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
ebi-gxa
parents: 4
diff changeset
22 #end if
87d54692a537 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
ebi-gxa
parents: 4
diff changeset
23 #if $include_sem_siml
4
32101a7373ae "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
24 --include-sem-siml "${include_sem_siml}"
32101a7373ae "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
25 #end if
1
a31bc9849f91 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
26 #if $parallel
a31bc9849f91 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
27 --parallel "${parallel}"
a31bc9849f91 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
28 #end if
4
32101a7373ae "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
29 #if $sort_by_agg_score
32101a7373ae "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
30 --sort-by-agg-score "${sort_by_agg_score}"
32101a7373ae "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
31 #end if
1
a31bc9849f91 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
32 #if $exclusions
a31bc9849f91 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
33 --exclusions "${exclusions}"
a31bc9849f91 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
34 #end if
5
87d54692a537 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
ebi-gxa
parents: 4
diff changeset
35 #if $sem_siml_metric
87d54692a537 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
ebi-gxa
parents: 4
diff changeset
36 --semantic-sim-metric "${sem_siml_metric}"
1
a31bc9849f91 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
37 #end if
a31bc9849f91 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
38 ]]></command>
0
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
39 <inputs>
2
94927cc336ba "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents: 1
diff changeset
40 <param type="data" name="input_tables" label="Aggregated tables" format="txt" multiple="true" help="Aggregated prediction tables from multiple tools" />
5
87d54692a537 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
ebi-gxa
parents: 4
diff changeset
41 <param type="data" name="tool_table" format="txt" optional="true" label="Tool performance table" help="Table with tools performance metrics" />
0
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
42 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
4
32101a7373ae "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
43 <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" />
32101a7373ae "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
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?" />
32101a7373ae "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
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?" />
0
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
46 <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
47 <param type="data" name="lab_cl_mapping" format="rdata" label="cl terms mapping" help="Label - CL term mapping" />
4
32101a7373ae "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
48 <param type="data" name="ontology_graph" format="obo" label="Ontology graph" optional="true" help="Ontology graph to run similairty calculations" />
32101a7373ae "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
49 <expand macro="sem_siml_options" />
0
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
50 </inputs>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
51 <outputs>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
52 <data name="summary_table_output_path" format="txt" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
53 <data name="raw_table_output_path" format="txt" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
54 </outputs>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
55 <tests>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
56 <test>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
57 <param name="input_tables" value="prod_combined_tools/scmap_combined.tsv,prod_combined_tools/scpred_combined.tsv" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
58 <param name="tool_table" value="tool_perf_pvals.tsv" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
59 <param name="exclusions" value="exclusions.yml" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
60 <param name="parallel" value="TRUE" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
61 <param name="lab_cl_mapping" value="label_cl_dict.rds" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
62 <param name="ontology_graph" value="cl-basic.obo" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
63 <output name="summary_table_output_path" file="summary_output_table.tsv" compare="sim_size" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
64 <output name="raw_table_output_path" file="raw_labels_table.tsv" compare="sim_size" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
65 </test>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
66 </tests>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
67 <help><![CDATA[
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
68 @HELP@
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
69
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
70 @VERSION_HISTORY@
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
71 ]]></help>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
72 <expand macro="citations" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
73 </tool>