Mercurial > repos > iuc > data_manager_bakta

annotate data_manager/bakta_build_database.xml @ 3:c0bd27c2bc9b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
author iuc
date Fri, 23 Jun 2023 21:36:52 +0000
parents a84adf8c8a4a
children ba7b35caf55c
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a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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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>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code">
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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 '$__tool_directory__/bakta_build_database.py'
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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10 '$output_file'
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11 --database_version '$database_select'
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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>
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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)">
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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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>
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c0bd27c2bc9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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23 <option value="5.0">V5.0_2023-02-20</option>
c0bd27c2bc9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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24 <option value="5.0_light">V5.0_light_2023-02-20</option>
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a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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25 </param>
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26 <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
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27 </inputs>
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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28 <outputs>
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29 <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
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30 </outputs>
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31 <tests>
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32 <!-- Test 1 with version 1.0 -->
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33 <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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34 <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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35 <param name="database_select" value="1.0"/>
3
c0bd27c2bc9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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36 <output name="output_file" value="bakta_test_data_manager1.json" />
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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>
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38 <!-- 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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39 <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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40 <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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41 <param name="database_select" value="latest"/>
3
c0bd27c2bc9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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42 <output name="output_file" value="bakta_test_data_manager2.json" />
c0bd27c2bc9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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43 </test>
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44 <!-- Test 3 with light db -->
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45 <test expect_num_outputs="1">
c0bd27c2bc9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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46 <param name="test_data_manager" value="--test"/>
c0bd27c2bc9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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47 <param name="database_select" value="5.0_light"/>
c0bd27c2bc9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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48 <output name="output_file" value="bakta_test_data_manager3.json" />
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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49 </test>
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50 </tests>
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51 <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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52 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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53 ]]></help>
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54 <citations>
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55 <citation type="doi">10.1099/mgen.0.000685</citation>
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56 </citations>
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57 </tool>