Mercurial > repos > pimarin > data_manager_bakta

annotate data_manager/bakta_build_database.xml @ 9:683b09c92299 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4e0fa611488db8c2c30a5f332eef86fcf24c13af-dirty
author pimarin
date Thu, 27 Oct 2022 15:26:46 +0000
parents a1cd2e86adbf
children c50e8b4f74d7
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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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2 <tool id="bakta_build_database" name="Bakta" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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3 <description> Bakta database builder </description>
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4 <macros>
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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>
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7 <expand macro="requirements"/>
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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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10 <command detect_errors="aggressive"><![CDATA[
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47a3aac8fcf7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4e0fa611488db8c2c30a5f332eef86fcf24c13af-dirty
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11 mkdir './output_dir_json' &&
47a3aac8fcf7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4e0fa611488db8c2c30a5f332eef86fcf24c13af-dirty
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12 ln -s '$output_file' './output_dir_json/json_output.json' &&
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9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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13 python '$__tool_directory__/bakta_build_database.py'
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683b09c92299 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4e0fa611488db8c2c30a5f332eef86fcf24c13af-dirty
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14 './output_dir_json/json_output.json'
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15 --database_version '$database_select'
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16 ]]></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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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)" >
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19 <option value="latest" selected="true" > Latest available version </option>
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20 <option value="1.0"> V1.0_2020-11-20 </option>
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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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>
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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23 <option value="3.0"> V3.0_2021-08-05 </option>
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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24 <option value="3.1"> V3.1_2022-02-03 </option>
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25 <option value="4.0"> V4.0_2022-08-29 </option>
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26 <option value="test"> database_test </option>
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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27 </param>
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28 </inputs>
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29 <outputs>
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30 <data name="output_file" format="data_manager_json" from_work_dir="./output_dir_json/json_output.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="database_select" value="test"/>
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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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>
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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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>