Mercurial > repos > ebi-gxa > ct_combine_tool_outputs
diff ct_combine_tool_outputs.xml @ 0:7c7d1ef36bf6 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
| author | ebi-gxa |
|---|---|
| date | Wed, 08 Apr 2020 11:34:35 -0400 |
| parents | |
| children | a565cf41330b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ct_combine_tool_outputs.xml Wed Apr 08 11:34:35 2020 -0400 @@ -0,0 +1,37 @@ +<tool id="ct_combine_tool_outputs" name="Cell types - combine tools outputs" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>Combine predictions for single tool from multiple datasets</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 + + combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --exclusions "${exclusions}" --scores "${scores}" --output-table "${output_table}" ]]></command> + <inputs> + <param type="data" name="input_tables" label="Tables with predicted labels" multiple="true" format="tsv" help="Standardised tables obtained from multiple classifiers" /> + <param type="integer" name="top_labels_num" label="Number of top labels" value='3' help="Number of top labels to select" /> + <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" /> + <param type="boolean" name="scores" label="scores" checked="false" help="Are scores included into the tool outpus?" /> + </inputs> + <outputs> + <data name="output_table" format="tsv" /> + </outputs> + <tests> + <test> + <param name="input_tables" value="prod_outputs_scpred/E-MTAB-6386_scpred_final-labs.tsv,prod_outputs_scpred/OTHER-DATASET_scpred_final-labs.tsv" /> + <param name="scores" value="TRUE" /> + <param name="exclusions" value="exclusions.yml" /> + <output name="output_table" file="combined_results.tsv" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ + @HELP@ + + @VERSION_HISTORY@ + ]]></help> + <expand macro="citations" /> +</tool>