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annotate ct_get_consensus_outputs.xml @ 0:66cdd8438ac6 draft

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"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 11:34:17 -0400
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children a31bc9849f91
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66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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1 <tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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2 <description>Get consensus outputs across multiple tools</description>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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3 <macros>
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4 <import>ct_macros.xml</import>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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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[
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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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
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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13 ln -s $'${ontology_graph}' cl-basic.obo;
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14
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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15 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>
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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16 <inputs>
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17 <param type="data" name="input_tables" label="Aggregated tables" format="tsv" multiple="true" help="Aggregated prediction tables from multiple tools" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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18 <param type="data" name="tool_table" format="tsv" label="Tools table" help="Table with tools performance metrics" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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19 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
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20 <param type="integer" name="num_cores" value='4' label="Number of cores" help="Number of cores to run the process" />
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21 <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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22 <param type="data" name="lab_cl_mapping" format="rdata" label="cl terms mapping" help="Label - CL term mapping" />
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23 <param type="data" name="ontology_graph" format="obo" label="Ontology graph" help="Ontology graph to run similairty calculations" />
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24 <param type="text" name="semantic_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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25 </inputs>
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26 <outputs>
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27 <data name="summary_table_output_path" format="txt" />
66cdd8438ac6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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28 <data name="raw_table_output_path" format="txt" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input_tables" value="prod_combined_tools/scmap_combined.tsv,prod_combined_tools/scpred_combined.tsv" />
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33 <param name="tool_table" value="tool_perf_pvals.tsv" />
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34 <param name="exclusions" value="exclusions.yml" />
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35 <param name="parallel" value="TRUE" />
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36 <param name="lab_cl_mapping" value="label_cl_dict.rds" />
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37 <param name="ontology_graph" value="cl-basic.obo" />
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38 <output name="summary_table_output_path" file="summary_output_table.tsv" compare="sim_size" />
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39 <output name="raw_table_output_path" file="raw_labels_table.tsv" compare="sim_size" />
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 @HELP@
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44
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45 @VERSION_HISTORY@
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46 ]]></help>
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47 <expand macro="citations" />
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48 </tool>