Mercurial > repos > ebi-gxa > ct_get_tool_perf_table
view ct_get_tool_perf_table.xml @ 5:424f8251a202 draft
"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 07:24:58 -0400 |
parents | d15f7509077b |
children | 90d7f30478ee |
line wrap: on
line source
<tool id="ct_get_tool_perf_table" name="Cell types - get tool performance table" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>Get performance table for a list of outputs generated by various tools</description> <macros> <import>ct_macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ mkdir -p input_dir; #for $input_file in $input_files: cp '$input_file' input_dir/; #end for get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --num-cores \${GALAXY_SLOTS:-1} --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}" #if $exclusions --exclusions "${exclusions}" #end if #if $ontology_graph --ontology-graph "${ontology_graph}" #end if #if $parallel --parallel "${parallel}" #end if #if $tmpdir --tmpdir "${tmpdir}" #end if #if $include_sem_siml --include-sem-siml "${include_sem_siml}" #end if #if $barcode_col_ref --barcode-col-ref "${barcode_col_ref}" #end if #if $barcode_col_pred --barcode-col-pred "${barcode_col_pred}" #end if #if $label_col_ref --label-column-ref "${label_col_ref}" #end if #if $label_col_pred --label-column-pred "${label_col_pred}" #end if #if $sem_siml_metric --semantic-sim-metric "${sem_siml_metric}" #end if ]]></command> <inputs> <param type="data" name="input_files" label="Input tables" multiple="true" format="txt" help="Classification tables obtained from multiple classisifiers" /> <param type="data" name="ref_file" label="Reference metadata file" format="txt" help="Metadata file with reference labels" /> <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" /> <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="data" name="exclusions" label="Exclusions" format="yml" optional="true" help="Config file with exclusions" /> <param type="data" name="ontology_graph" label="Ontology graph" optional="true" format="obo" help="Ontology graph to run semantis similarity computations" /> <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" /> <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" /> <param type="text" name="barcode_col_ref" label="Reference file barcode field" value='cell_id' help="Name of barcode field in reference metadata file" /> <param type="text" name="barcode_col_pred" label="Predicted file barcode field" value="cell_id" help="Name of barcode field in predictions file" /> <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" /> <param type="text" name="label_col_pred" label="Predicted file label column" value="predicted_label" help="Name of label field in predictions file" /> <expand macro="sem_siml_options" /> </inputs> <outputs> <data name="output_path" format="txt" /> </outputs> <tests> <test> <param name="input_files" value="results_dir/garnett_output.txt,results_dir/scmap-cell_output.txt,results_dir/scmap-cluster_output.txt,results_dir/scpred_output.txt" /> <param name="ref_file" value="reference_sdrf.tsv" /> <param name="ontology_graph" value="cl-basic.obo" /> <param name="lab_cl_mapping" value="label_cl_dict.rds" /> <param name="parallel" value="TRUE" /> <param name="exclusions" value="exclusions.yml" /> <param name="barcode_col_ref" value="Assay" /> <param name="barcode_col_pred" value="cell_id" /> <param name="label_col_ref" value="Sample.Characteristic.cell.type." /> <param name="label_col_pred" value="predicted_label" /> <output name="output_path" file="tool_perf_table.tsv" compare="sim_size" /> </test> </tests> <help><![CDATA[ @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations" /> </tool>