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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 13:37:40 +0000
parents f2e01e023137
children
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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>for single tool from multiple datasets</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 combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --scores "${scores}" --output-table "${output_table}"
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15 #if $exclusions
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16 --exclusions "${exclusions}"
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17 #end if
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18 ]]></command>
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19 <inputs>
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20 <param type="data" name="input_tables" label="Tables with predicted labels" multiple="true" format="txt" help="Standardised tables obtained from multiple classifiers" />
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21 <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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22 <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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23 <param type="boolean" name="scores" label="scores" checked="false" help="Are scores included into the tool outpus?" />
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24 </inputs>
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25 <outputs>
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26 <data name="output_table" format="txt" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input_tables" value="prod_outputs_scpred/E-ENAD-27_scpred.txt,prod_outputs_scpred/E-GEOD-81608_scpred.txt" />
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31 <param name="scores" value="TRUE" />
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32 <param name="exclusions" value="exclusions.yml" />
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33 <output name="output_table" file="combined_results.tsv" compare="sim_size" />
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 @HELP@
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38
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39 @VERSION_HISTORY@
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40 ]]></help>
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41 <expand macro="citations" />
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42 </tool>