Mercurial > repos > pimarin > data_manager_fetch_plasmidfinder

annotate data_manager/plasmidfinder_fetch_database.xml @ 5:60cfd33bc2fb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit 0a3992c5be846fc9f18b7ca18f0adcd78f5b9396-dirty
author pimarin
date Mon, 24 Jul 2023 10:00:33 +0000
parents 5ffc68b4ec04
children 4e933a39094f
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8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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1 <tool id="data_manager_fetch_plasmidfinder" name="plasmidfinder_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>plasmidfinder database builder</description>
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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3 <macros>
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4 <import>macro.xml</import>
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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5 </macros>
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6 <expand macro="requirements"/>
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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7 <command detect_errors="exit_code">
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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8 <![CDATA[
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9 python '$__tool_directory__/plasmidfinder_fetch_database.py'
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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10 --db_version '$database_select'
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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11 '$output_file'
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12 && cat '$output_file'
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13 ]]></command>
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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14 <inputs>
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15 <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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16 <option value="latest" selected="true">Latest available version</option>
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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17 <option value="2.1">V2.1_2019-08-28</option>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data name="output_file" format="data_manager_json"/>
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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22 </outputs>
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23 <tests>
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24 <!-- Test_2 DB 2.1 -->
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25 <test expect_num_outputs="1">
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60cfd33bc2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit 0a3992c5be846fc9f18b7ca18f0adcd78f5b9396-dirty
pimarin
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26 <param name="database_select" value="2.1"/>
60cfd33bc2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit 0a3992c5be846fc9f18b7ca18f0adcd78f5b9396-dirty
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27 <output name="output_file" value="plasmidfinder_test_data_manager_2.1.json">
60cfd33bc2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit 0a3992c5be846fc9f18b7ca18f0adcd78f5b9396-dirty
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28 <assert_contents>
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29 <has_text text="2019_08_28"/>
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30 </assert_contents>
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31 </output>
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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60cfd33bc2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit 0a3992c5be846fc9f18b7ca18f0adcd78f5b9396-dirty
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35 Download plasmidfinder database from the bitbucket repository: https://bitbucket.org/genomicepidemiology/plasmidfinder_db/src/master/
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36 ]]></help>
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37 <citations>
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38 <citation type="doi">10.1007/978-1-4939-9877-7_20</citation>
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39 </citations>
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40 </tool>