Mercurial > repos > ebi-gxa > ct_get_consensus_outputs
changeset 7:0917f5e09d83 draft default tip
"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 | |
| files | ct_get_consensus_outputs.xml ct_macros.xml |
| diffstat | 2 files changed, 22 insertions(+), 16 deletions(-) [+] |
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--- a/ct_get_consensus_outputs.xml Thu Jul 23 11:56:13 2020 -0400 +++ b/ct_get_consensus_outputs.xml Fri Nov 27 13:38:17 2020 +0000 @@ -1,5 +1,5 @@ -<tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@"> - <description>Get consensus outputs across multiple tools</description> +<tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>across multiple tools</description> <macros> <import>ct_macros.xml</import> </macros> @@ -10,22 +10,16 @@ cp '$table' input_dir/; #end for - get_consensus_output.R --input-dir input_dir --num-cores \${GALAXY_SLOTS:-1} --cl-dictionary "${lab_cl_mapping}" --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}" + 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 ./ #if $tool_table --tool-table "${tool_table}" #end if #if $ontology_graph --ontology-graph "${ontology_graph}" #end if - #if $tmpdir - --tmpdir "${tmpdir}" - #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 @@ -35,17 +29,19 @@ #if $sem_siml_metric --semantic-sim-metric "${sem_siml_metric}" #end if + #if $true_labels + --true-labels "${true_labels}" + #end if ]]></command> <inputs> <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" optional="true" label="Tool performance 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" optional="true" help="Ontology graph to run similairty calculations" /> + <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" /> <expand macro="sem_siml_options" /> </inputs> <outputs> @@ -54,12 +50,10 @@ </outputs> <tests> <test> - <param name="input_tables" value="prod_combined_tools/scmap_combined.tsv,prod_combined_tools/scpred_combined.tsv" /> + <param name="input_tables" value="prod_combined_tools/scmap-cell.txt,prod_combined_tools/scmap-cluster.txt,prod_combined_tools/scpred.txt" /> <param name="tool_table" value="tool_perf_pvals.tsv" /> <param name="exclusions" value="exclusions.yml" /> - <param name="parallel" value="TRUE" /> <param name="lab_cl_mapping" value="label_cl_dict.rds" /> - <param name="ontology_graph" value="cl-basic.obo" /> <output name="summary_table_output_path" file="summary_output_table.tsv" compare="sim_size" /> <output name="raw_table_output_path" file="raw_labels_table.tsv" compare="sim_size" /> </test>
--- a/ct_macros.xml Thu Jul 23 11:56:13 2020 -0400 +++ b/ct_macros.xml Fri Nov 27 13:38:17 2020 +0000 @@ -1,10 +1,10 @@ <macros> - <token name="@TOOL_VERSION@">1.1.0</token> + <token name="@TOOL_VERSION@">1.1.1</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="0.1.1">cell-types-analysis</requirement> + <requirement type="package" version="0.1.9">cell-types-analysis</requirement> <yield/> </requirements> </xml> @@ -15,6 +15,7 @@ </xml> <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** +0.1.6+galaxy0: Add removing non-alphanumeric characters from labels in metadata files 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> @@ -34,6 +35,17 @@ <option value="resnik">resnik</option> </param> </xml> + <xml name="sanitize_strings"> + <sanitizer invalid_char=""> + <valid initial="string.ascii_letters,string.digits"> + <add value="_" /> + <add value="-" /> + <add value="[" /> + <add value="]" /> + <add value=" " /> + </valid> + </sanitizer> + </xml> <xml name="citations"> <citations> <citation type="bibtex">