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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 11:34:35 -0400
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children a565cf41330b
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7c7d1ef36bf6 "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_combine_tool_outputs" name="Cell types - combine tools outputs" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>Combine predictions for single tool from multiple datasets</description>
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3 <macros>
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4 <import>ct_macros.xml</import>
7c7d1ef36bf6 "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[
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8 mkdir -p input_dir;
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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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
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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13 combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --exclusions "${exclusions}" --scores "${scores}" --output-table "${output_table}" ]]></command>
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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14 <inputs>
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15 <param type="data" name="input_tables" label="Tables with predicted labels" multiple="true" format="tsv" help="Standardised tables obtained from multiple classifiers" />
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16 <param type="integer" name="top_labels_num" label="Number of top labels" value='3' help="Number of top labels to select" />
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17 <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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18 <param type="boolean" name="scores" label="scores" checked="false" help="Are scores included into the tool outpus?" />
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19 </inputs>
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20 <outputs>
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21 <data name="output_table" format="tsv" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input_tables" value="prod_outputs_scpred/E-MTAB-6386_scpred_final-labs.tsv,prod_outputs_scpred/OTHER-DATASET_scpred_final-labs.tsv" />
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26 <param name="scores" value="TRUE" />
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27 <param name="exclusions" value="exclusions.yml" />
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28 <output name="output_table" file="combined_results.tsv" compare="sim_size" />
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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29 </test>
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30 </tests>
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31 <help><![CDATA[
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32 @HELP@
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33
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34 @VERSION_HISTORY@
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35 ]]></help>
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36 <expand macro="citations" />
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37 </tool>