Mercurial > repos > pimarin > data_manager_bakta

annotate data_manager/bakta_build_database.xml @ 14:bcac3aa1f494 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit b082e89a0090f9c4b2a257bb06b7c6f141b42650-dirty
author pimarin
date Wed, 02 Nov 2022 16:14:09 +0000
parents 8f63e424da2b
children 718080c30a76
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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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1 <tool id="bakta_build_database" name="Bakta" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Bakta database builder</description>
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3 <macros>
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4 <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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5 </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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6 <expand macro="requirements"/>
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7
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8 <command detect_errors="exit_code">
7bd60bfa8ffc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit b082e89a0090f9c4b2a257bb06b7c6f141b42650-dirty
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9 <![CDATA[
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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 python '$__tool_directory__/bakta_build_database.py'
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11 '$output_file'
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12 --database_version '$database_select'
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7bd60bfa8ffc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit b082e89a0090f9c4b2a257bb06b7c6f141b42650-dirty
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13 #if '$test_data_manager' != ''
7bd60bfa8ffc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit b082e89a0090f9c4b2a257bb06b7c6f141b42650-dirty
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14 '$test_data_manager'
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15 #end if
7bd60bfa8ffc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit b082e89a0090f9c4b2a257bb06b7c6f141b42650-dirty
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16 ]]></command>
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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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17 <inputs>
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18 <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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19 <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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20 <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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21 <option value="1.1">V1.1_2020-12-18</option>
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22 <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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23 <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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24 <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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25 <option value="4.0">V4.0_2022-08-29</option>
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26 </param>
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27 <param name="test_data_manager" type="hidden" value=""/>
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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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28 </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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29 <outputs>
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30 <data name="output_file" format="data_manager_json"/>
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31 </outputs>
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32 <tests>
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33 <!-- Test download -->
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34 <test expect_num_outputs="1">
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35 <param name="test_data_manager" value="--test"/>
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36 <output name="output_file" value="bakta_test_data_manager.json" compare="contains"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 Download specific version of Bakta database <https://github.com/oschwengers/bakta#database>
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41 ]]></help>
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42 <citations>
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43 <citation type="doi">10.1099/mgen.0.000685</citation>
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44 </citations>
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45 </tool>