| Next changeset 1:a31bc9849f91 (2020-04-24) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2" |
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added:
ct_get_consensus_outputs.xml ct_macros.xml |
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| diff -r 000000000000 -r 66cdd8438ac6 ct_get_consensus_outputs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ct_get_consensus_outputs.xml Wed Apr 08 11:34:17 2020 -0400 |
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| @@ -0,0 +1,48 @@ +<tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>Get consensus outputs across multiple tools</description> + <macros> + <import>ct_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + mkdir -p input_dir; + #for $table in $input_tables: + cp '$table' input_dir/; + #end for + + ln -s $'${ontology_graph}' cl-basic.obo; + + get_consensus_output.R --input-dir input_dir --tool-table "${tool_table}" --num-cores "${num_cores}" --cl-dictionary "${lab_cl_mapping}" --parallel "${parallel}" --exclusions "${exclusions}" --ontology-graph cl-basic.obo --semantic-sim-metric "${semantic_sim_metric}" --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}" ]]></command> + <inputs> + <param type="data" name="input_tables" label="Aggregated tables" format="tsv" multiple="true" help="Aggregated prediction tables from multiple tools" /> + <param type="data" name="tool_table" format="tsv" 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="integer" name="num_cores" value='4' label="Number of cores" help="Number of cores to run the process" /> + <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" /> + </inputs> + <outputs> + <data name="summary_table_output_path" format="txt" /> + <data name="raw_table_output_path" format="txt" /> + </outputs> + <tests> + <test> + <param name="input_tables" value="prod_combined_tools/scmap_combined.tsv,prod_combined_tools/scpred_combined.tsv" /> + <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> + </tests> + <help><![CDATA[ + @HELP@ + + @VERSION_HISTORY@ + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 66cdd8438ac6 ct_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ct_macros.xml Wed Apr 08 11:34:17 2020 -0400 |
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| @@ -0,0 +1,35 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.0</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> + <yield/> + </requirements> + </xml> + <xml name="version"> + <version_command><![CDATA[ + conda list | grep cell-types-analysis | egrep -o [0-9]\.[0-9]\.[0-9] + ]]></version_command> + </xml> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** +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/. + ]]></token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{github-cell-types-analysis.git, + author = {Andrey Solovyev, EBI Gene Expression Team}, + year = {2020}, + title = {Suite of scripts for analysis of scRNA-seq cell type classification tool outputs}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/cell-types-analysis.git}, + } + </citation> + <yield /> + </citations> + </xml> +</macros> \ No newline at end of file |