Previous changeset 3:559fbff1f573 (2020-04-27) Next changeset 5:87d54692a537 (2020-07-13) |
Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1" |
modified:
ct_get_consensus_outputs.xml ct_macros.xml |
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diff -r 559fbff1f573 -r 32101a7373ae ct_get_consensus_outputs.xml --- a/ct_get_consensus_outputs.xml Mon Apr 27 11:12:14 2020 -0400 +++ b/ct_get_consensus_outputs.xml Wed Jun 17 12:29:44 2020 -0400 |
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@@ -16,9 +16,15 @@ #if $tool_table --tool-table "${tool_table}" #end if + #if $include-sem-siml + --include-sem-siml "${include_sem_siml}" + #end if #if $parallel --parallel "${parallel}" #end if + #if $sort_by_agg_score + --sort-by-agg-score "${sort_by_agg_score}" + #end if #if $exclusions --exclusions "${exclusions}" #end if @@ -30,10 +36,13 @@ <param type="data" name="input_tables" label="Aggregated tables" format="txt" multiple="true" help="Aggregated prediction tables from multiple tools" /> <param type="data" name="tool_table" format="txt" label="Tools table" help="Table with tools performance metrics" /> <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" /> + <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" /> + <param type="boolean" name="include_sem_siml" label="Include Semantic Similarity" checked="false" help="Should semantic similarity be included in calculation of combined score?" /> + <param type="boolean" name="sort_by_agg_score" label="Sort by aggregated score" checked="true" help="Should the cells be ordered by aggregated score?" /> <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" /> <param type="data" name="lab_cl_mapping" format="rdata" label="cl terms mapping" help="Label - CL term mapping" /> - <param type="data" name="ontology_graph" format="obo" label="Ontology graph" help="Ontology graph to run similairty calculations" /> - <param type="text" name="semantic_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" /> + <param type="data" name="ontology_graph" format="obo" label="Ontology graph" optional="true" help="Ontology graph to run similairty calculations" /> + <expand macro="sem_siml_options" /> </inputs> <outputs> <data name="summary_table_output_path" format="txt" /> |
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diff -r 559fbff1f573 -r 32101a7373ae ct_macros.xml --- a/ct_macros.xml Mon Apr 27 11:12:14 2020 -0400 +++ b/ct_macros.xml Wed Jun 17 12:29:44 2020 -0400 |
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@@ -1,10 +1,10 @@ <macros> - <token name="@TOOL_VERSION@">1.0.0</token> + <token name="@TOOL_VERSION@">1.1.0</token> <token name="@HELP@">More information can be found at https://github.com/ebi-gene-expression-group/cell-types-analysis</token> <token name="@PROFILE@">18.01</token> <xml name="requirements"> <requirements> - <requirement type="package" version="0.0.8">cell-types-analysis</requirement> + <requirement type="package" version="0.1.1">cell-types-analysis</requirement> <yield/> </requirements> </xml> @@ -18,6 +18,22 @@ 0.0.5+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/. 0.0.5+galaxy1: Standardise input/output format into .txt. ]]></token> + <xml name="sem_siml_options"> + <param type="select" name="sem_siml_metric" label="Semantic similarity metric" help="What semantic similarity metric should be used? NB: if include-sem-siml is set to True, make sure to use a metric that is in the [0;1] interval. See https://www.bioconductor.org/packages/release/bioc/html/Onassis.html for more detail."> + <option value="lin" selected="true">lin</option> + <option value="jaccard">jaccard</option> + <option value="jc_norm">jc_norm</option> + <option value="schlicker">schlicker</option> + <option value="edge_resnik">edge_resnik</option> + <option value="sim">sim</option> + <option value="edge_leachod">edge_leachod</option> + <option value="edge_slimani">edge_slimani</option> + <option value="edge_wupalmer">edge_wupalmer</option> + <option value="edge_rada_lca">edge_rada_lca</option> + <option value="edge_li">edge_li</option> + <option value="resnik">resnik</option> + </param> + </xml> <xml name="citations"> <citations> <citation type="bibtex"> |