Mercurial > repos > pimarin > abromics_extractor_summarize

annotate abromics_galaxy_json_extractor_summarize.xml @ 2:5a7db3d820c5 draft

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author pimarin
date Wed, 05 Jul 2023 14:22:57 +0000
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1 <tool id="abromics_extractor_summarize" name="abromics_extractor_summarize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>
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3 Summarize results from abromicsextractor
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4 </description>
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5 <macros>
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6 <import>macro.xml</import>
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7 </macros>
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8 <expand macro='edam'/>
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9 <expand macro="requirements"/>
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10 <expand macro="version_command"/>
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11 <command detect_errors="aggressive"><![CDATA[
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12 mkdir -p input_files &&
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13 #for $file in $summarize_data
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14 cp $file input_files &&
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15 #end for
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16 abromics_extract summarize input_files/* -o abromics_summary.json
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="summarize_data" type="data" multiple="true" format="json" label="Results in Json format" help="Summarize results from abromicsextractor in json format"/>
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21 </inputs>
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22 <outputs>
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23 <data name="summary_json" format="json" from_work_dir="abromics_summary.json" label="${tool.name} on ${on_string}: Summarized file"/>
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24 </outputs>
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25 <tests>
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26 <test expect_num_outputs="1"> <!-- TEST_1 sumarize json results -->
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27 <param name="summarize_data" ftype="json" value="summarize/abricate_output.json,summarize/bracken_full_output.json,summarize/plasmidfinder_output.json"/>
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28 <output name="summary_json" ftype="json" value="summarize/summarize.json" compare="sim_size"/>
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29 </test>
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30 </tests>
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31 <help><![CDATA[**What it does**
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32 Summarize Json output file from abromics_galaxy_json_extractor to only one json file
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33 ]]></help>
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34 <expand macro="citations"/>
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35 </tool>