Mercurial > repos > ebi-gxa > ct_get_consensus_outputs

annotate ct_get_consensus_outputs.xml @ 4:32101a7373ae draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
author ebi-gxa
date Wed, 17 Jun 2020 12:29:44 -0400
parents 559fbff1f573
children 87d54692a537
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1 <tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>Get consensus outputs 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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13 ln -s $'${ontology_graph}' cl-basic.obo;
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14
1
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15 get_consensus_output.R --input-dir input_dir --num-cores \${GALAXY_SLOTS:-1} --cl-dictionary "${lab_cl_mapping}" --ontology-graph cl-basic.obo --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}"
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16 #if $tool_table
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17 --tool-table "${tool_table}"
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18 #end if
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19 #if $include-sem-siml
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20 --include-sem-siml "${include_sem_siml}"
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21 #end if
1
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22 #if $parallel
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23 --parallel "${parallel}"
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24 #end if
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25 #if $sort_by_agg_score
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26 --sort-by-agg-score "${sort_by_agg_score}"
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27 #end if
1
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28 #if $exclusions
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29 --exclusions "${exclusions}"
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30 #end if
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31 #if $semantic_sim_metric
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32 --semantic-sim-metric "${semantic_sim_metric}"
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33 #end if
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34 ]]></command>
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35 <inputs>
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36 <param type="data" name="input_tables" label="Aggregated tables" format="txt" multiple="true" help="Aggregated prediction tables from multiple tools" />
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37 <param type="data" name="tool_table" format="txt" label="Tools table" help="Table with tools performance metrics" />
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38 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
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39 <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" />
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40 <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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41 <param type="boolean" name="sort_by_agg_score" label="Sort by aggregated score" checked="true" help="Should the cells be ordered by aggregated score?" />
0
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42 <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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43 <param type="data" name="lab_cl_mapping" format="rdata" label="cl terms mapping" help="Label - CL term mapping" />
4
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44 <param type="data" name="ontology_graph" format="obo" label="Ontology graph" optional="true" help="Ontology graph to run similairty calculations" />
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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_combined.tsv,prod_combined_tools/scpred_combined.tsv" />
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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="parallel" value="TRUE" />
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57 <param name="lab_cl_mapping" value="label_cl_dict.rds" />
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58 <param name="ontology_graph" value="cl-basic.obo" />
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59 <output name="summary_table_output_path" file="summary_output_table.tsv" compare="sim_size" />
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60 <output name="raw_table_output_path" file="raw_labels_table.tsv" compare="sim_size" />
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64 @HELP@
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65
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66 @VERSION_HISTORY@
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67 ]]></help>
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68 <expand macro="citations" />
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69 </tool>