Mercurial > repos > iuc > data_manager_bakta

annotate data_manager/bakta_build_database.xml @ 0:a84adf8c8a4a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
author iuc
date Sat, 10 Dec 2022 21:52:13 +0000
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a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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1 <tool id="bakta_build_database" name="Bakta" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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2 <description>Bakta database builder</description>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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3 <macros>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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4 <import>macro.xml</import>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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5 </macros>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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6 <expand macro="requirements"/>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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7 <command detect_errors="exit_code">
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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8 <![CDATA[
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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9 python '$__tool_directory__/bakta_build_database.py'
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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10 '$output_file'
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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11 --database_version '$database_select'
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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12 $test_data_manager
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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13 ]]></command>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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14 <inputs>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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15 <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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16 <option value="latest" selected="true">Latest available version</option>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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17 <option value="1.0">V1.0_2020-11-20</option>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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18 <option value="1.1">V1.1_2020-12-18</option>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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19 <option value="2.0">V2.0_2021-04-05</option>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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20 <option value="3.0">V3.0_2021-08-05</option>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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21 <option value="3.1">V3.1_2022-02-03</option>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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22 <option value="4.0">V4.0_2022-08-29</option>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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23 </param>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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24 <param name="test_data_manager" type="hidden" value=""/>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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25 </inputs>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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26 <outputs>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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27 <data name="output_file" format="data_manager_json"/>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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28 </outputs>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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29 <tests>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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30 <!-- Test 1 with version 1.0 -->
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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31 <test expect_num_outputs="1">
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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32 <param name="test_data_manager" value="--test"/>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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33 <param name="database_select" value="1.0"/>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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34 <output name="output_file" value="bakta_test_data_manager.json" />
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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35 </test>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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36 <!-- Test 2 with the latest option -->
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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37 <test expect_num_outputs="1">
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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38 <param name="test_data_manager" value="--test"/>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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39 <param name="database_select" value="latest"/>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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40 <output name="output_file" value="bakta_test_data_manager_test2.json" />
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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41 </test>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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42 </tests>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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43 <help><![CDATA[
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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44 Download specific version of Bakta database <https://github.com/oschwengers/bakta#database>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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45 ]]></help>
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46 <citations>
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47 <citation type="doi">10.1099/mgen.0.000685</citation>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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48 </citations>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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49 </tool>