Mercurial > repos > ebi-gxa > ct_get_consensus_outputs

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"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
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1 <tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>across multiple tools</description>
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3 <macros>
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4 <import>ct_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 mkdir -p input_dir;
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9 #for $table in $input_tables:
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10 cp '$table' input_dir/;
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11 #end for
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12
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13 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 ./
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14 #if $tool_table
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15 --tool-table "${tool_table}"
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16 #end if
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17 #if $ontology_graph
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18 --ontology-graph "${ontology_graph}"
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19 #end if
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20 #if $include_sem_siml
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21 --include-sem-siml "${include_sem_siml}"
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22 #end if
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23 #if $sort_by_agg_score
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24 --sort-by-agg-score "${sort_by_agg_score}"
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25 #end if
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26 #if $exclusions
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27 --exclusions "${exclusions}"
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28 #end if
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29 #if $sem_siml_metric
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30 --semantic-sim-metric "${sem_siml_metric}"
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31 #end if
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32 #if $true_labels
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33 --true-labels "${true_labels}"
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34 #end if
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35 ]]></command>
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36 <inputs>
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37 <param type="data" name="input_tables" label="Aggregated tables" format="txt" multiple="true" help="Aggregated prediction tables from multiple tools" />
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38 <param type="data" name="tool_table" format="txt" optional="true" label="Tool performance table" help="Table with tools performance metrics" />
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39 <param type="boolean" name="include_sem_siml" label="Include Semantic Similarity" checked="false" help="Should semantic similarity be included in calculation of combined score?" />
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40 <param type="boolean" name="sort_by_agg_score" label="Sort by aggregated score" checked="true" help="Should the cells be ordered by aggregated score?" />
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41 <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" />
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42 <param type="data" name="lab_cl_mapping" format="rdata" label="cl terms mapping" help="Label - CL term mapping" />
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43 <param type="data" name="ontology_graph" format="obo" label="Ontology graph" optional="true" help="Ontology graph to run similairty calculations" />
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44 <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" />
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45 <expand macro="sem_siml_options" />
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46 </inputs>
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47 <outputs>
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48 <data name="summary_table_output_path" format="txt" />
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49 <data name="raw_table_output_path" format="txt" />
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="input_tables" value="prod_combined_tools/scmap-cell.txt,prod_combined_tools/scmap-cluster.txt,prod_combined_tools/scpred.txt" />
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54 <param name="tool_table" value="tool_perf_pvals.tsv" />
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55 <param name="exclusions" value="exclusions.yml" />
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56 <param name="lab_cl_mapping" value="label_cl_dict.rds" />
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57 <output name="summary_table_output_path" file="summary_output_table.tsv" compare="sim_size" />
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58 <output name="raw_table_output_path" file="raw_labels_table.tsv" compare="sim_size" />
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59 </test>
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60 </tests>
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61 <help><![CDATA[
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62 @HELP@
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63
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64 @VERSION_HISTORY@
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65 ]]></help>
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66 <expand macro="citations" />
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67 </tool>