Mercurial > repos > pimarin > data_manager_bakta

annotate data_manager/bakta_build_database.xml @ 11:c50e8b4f74d7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
author pimarin
date Wed, 02 Nov 2022 11:06:36 +0000
parents 683b09c92299
children 7bd60bfa8ffc
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faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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2 <tool id="bakta_build_database" name="Bakta" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
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3 <description>Bakta database builder</description>
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4 <macros>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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5 <import>macro.xml</import>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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6 </macros>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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7 <expand macro="requirements"/>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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8 <expand macro="version_command"/>
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faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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10 <command detect_errors="aggressive"><![CDATA[
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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11 python '$__tool_directory__/bakta_build_database.py'
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c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
pimarin
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12 '$output_file'
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13 --database_version '$database_select'
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c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
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14 '$test_data_manager'
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15 ]]></command>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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16 <inputs>
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17 <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
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18 <option value="latest" selected="true">Latest available version</option>
c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
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19 <option value="1.0">V1.0_2020-11-20</option>
c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
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20 <option value="1.1">V1.1_2020-12-18</option>
c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
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21 <option value="2.0">V2.0_2021-04-05</option>
c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
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22 <option value="3.0">V3.0_2021-08-05</option>
c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
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23 <option value="3.1">V3.1_2022-02-03</option>
c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
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24 <option value="4.0">V4.0_2022-08-29</option>
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25 </param>
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c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
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26 <param name="test_data_manager" type="hidden" value=""/>
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27 </inputs>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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28 <outputs>
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c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
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29 <data name="output_file" format="data_manager_json"/>
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30 </outputs>
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31 <tests>
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32 <!-- Test download -->
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33 <test expect_num_outputs="1">
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c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
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34 <param name="test_data_manager" value="--test"/>
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faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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35 <output name="output_file" value="bakta_test_data_manager.json" compare="contains"/>
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36 </test>
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37 </tests>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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38 <help><![CDATA[
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39 Download specific version of Bakta database <https://github.com/oschwengers/bakta#database>
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40 ]]></help>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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41 <citations>
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42 <citation type="doi">10.1099/mgen.0.000685</citation>
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43 </citations>
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44 </tool>