Mercurial > repos > iuc > data_manager_gtdbtk_database_installer

annotate data_manager/gtdbtk_database_installer.xml @ 1:f54abc2f5707 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 196c4976945b02d23227836ae9cf70a9f44eed59
author iuc
date Tue, 03 Jan 2023 09:04:59 +0000
parents 3221e031d107
children 9dcb593e8a43
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3221e031d107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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1 <tool id="gtdbtk_database_installer" name="GTDB-Tk Database Installer" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description></description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">202</token>
3221e031d107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <token name="@PROFILE@">20.09</token>
3221e031d107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="3.10.2">python</requirement>
3221e031d107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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10 </requirements>
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11 <command>
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12 <![CDATA[
3221e031d107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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13 python '$__tool_directory__/gtdbtk_database_installer.py'
3221e031d107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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14 --database_id '$database_id'
3221e031d107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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15 --database_name '$database_name'
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16 --url '$url'
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17 --out_file '$out_file'
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18 ]]>
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19 </command>
3221e031d107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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20 <inputs>
3221e031d107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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21 <param name="database_name" type="text" value="" label="Database name or description" help="This value will be displayed in the GTDB-Tk Database select list"/>
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f54abc2f5707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 196c4976945b02d23227836ae9cf70a9f44eed59
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22 <param name="database_id" type="text" value="" label="Database id" help="This value must be unique with no whitespace allowed - use underscores"/>
f54abc2f5707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 196c4976945b02d23227836ae9cf70a9f44eed59
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23 <param
f54abc2f5707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 196c4976945b02d23227836ae9cf70a9f44eed59
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24 name="url"
f54abc2f5707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 196c4976945b02d23227836ae9cf70a9f44eed59
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25 type="text"
f54abc2f5707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 196c4976945b02d23227836ae9cf70a9f44eed59
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26 value="https://data.gtdb.ecogenomic.org/releases/release202/202.0/auxillary_files/gtdbtk_r202_data.tar.gz"
f54abc2f5707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 196c4976945b02d23227836ae9cf70a9f44eed59
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27 label="URL for GTDB release"
f54abc2f5707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 196c4976945b02d23227836ae9cf70a9f44eed59
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28 help="This should point to a GTDB release tarball. A table of available databases and their version compatability can be found at https://ecogenomics.github.io/GTDBTk/installing/index.html#gtdb-tk-reference-data."
f54abc2f5707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 196c4976945b02d23227836ae9cf70a9f44eed59
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29 />
0
3221e031d107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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30 </inputs>
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31 <outputs>
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32 <data name="out_file" format="data_manager_json"/>
3221e031d107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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33 </outputs>
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34 <tests>
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35 <test>
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36 <!-- Not actually installing a huge GTDB-Tk database -->
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37 <param name="database_id" value="release202"/>
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38 <param name="database_name" value="GTDB-Tk database release 202"/>
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39 <param name="url" value="https://data.gtdb.ecogenomic.org/releases/release202/202.0/VERSION"/>
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40 <output name="out_file">
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41 <assert_contents>
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42 <has_text text="GTDB-Tk database release 202"/>
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43 <has_text text="release202"/>
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44 </assert_contents>
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45 </output>
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46 </test>
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47 </tests>
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48 <help>
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49 </help>
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50 <citations>
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51 <citation type="doi">doi.org/10.1038/s41587-020-0501-8</citation>
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52 <citation type="doi">dx.doi.org/10.1038/nbt.4229</citation>
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53 </citations>
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54 </tool>