Mercurial > repos > iuc > data_manager_gtdbtk_database_installer

annotate data_manager/gtdbtk_database_installer.xml @ 5:e7b39a7e0024 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 5706be8dc8c4899f5fe3b65f226937bb486a9873
author iuc
date Thu, 05 Sep 2024 11:30:01 +0000
parents 10232d2b5062
children df84aaed4769
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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>
5
e7b39a7e0024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 5706be8dc8c4899f5fe3b65f226937bb486a9873
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5 <token name="@VERSION_SUFFIX@">1</token>
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6 <token name="@PROFILE@">20.09</token>
629464b96c2e 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>
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10 </requirements>
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11 <command>
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12 <![CDATA[
629464b96c2e 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 '$__tool_directory__/gtdbtk_database_installer.py'
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14 --database_name '$database_name'
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15 --release '$release'
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16 --out_file '$out_file'
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17 $meta
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18 $test
0
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19 ]]>
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20 </command>
629464b96c2e 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 <inputs>
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22 <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"/>
2
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23 <param name="meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Only store GTDBTK metadata in a dedicated data table. " />
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
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24 <param name="test" type="hidden" value="" checked="false" label="Run a dry test run !" />
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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25 <param name="release" type="select" multiple="false" label="GTDB Release">
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26 <option value="202">202</option>
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27 <option value="207">207</option>
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28 <option value="214">214</option>
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29 <option value="220">220</option>
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30 </param>
0
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31 </inputs>
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32 <outputs>
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33 <data name="out_file" format="data_manager_json"/>
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34 </outputs>
629464b96c2e 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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35 <tests>
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36 <test>
2
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37 <!-- TODO -->
0
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38 <!-- Not actually installing a huge GTDB-Tk database -->
4
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39 <!-- but it will check if all urls exist -->
2
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40 <param name="release" value="202"/>
0
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41 <param name="database_name" value="GTDB-Tk database release 202"/>
2
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42 <param name="test" value="--test"/>
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43 <output name="out_file">
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44 <assert_contents>
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45 <has_text text="GTDB-Tk database release 202"/>
4
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46 <has_text text="release_202"/>
2
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47 </assert_contents>
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48 </output>
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49 </test>
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50 <test>
4
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51 <!-- Test meta data download with tsv.gz-->
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52 <param name="release" value="220"/>
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53 <param name="database_name" value="GTDB-Tk database release 220 metadata"/>
2
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54 <param name="meta" value="true"/>
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55 <output name="out_file">
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56 <assert_contents>
4
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57 <has_text text="GTDB-Tk database release 220 metadata"/>
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58 <has_text text="release_220"/>
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59 </assert_contents>
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60 </output>
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61 </test>
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62 <test>
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63 <!-- Test meta data download with tar.gz -->
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64 <param name="release" value="207"/>
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65 <param name="database_name" value="GTDB-Tk database release 207 metadata"/>
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66 <param name="meta" value="true"/>
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67 <output name="out_file">
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68 <assert_contents>
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69 <has_text text="GTDB-Tk database release 207 metadata"/>
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70 <has_text text="release_207"/>
0
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71 </assert_contents>
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72 </output>
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73 </test>
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74 </tests>
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75 <help>
2
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76 This data manager downloads the DB required for GTDB-Tk tools such as
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
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77 the `gtdbtk classify_wf`. The meta options allows downloading only the metadata for the
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
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78 corresponding DB, which is used by tools like `gtdb_to_taxdump`.
0
629464b96c2e 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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79 </help>
629464b96c2e 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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80 <citations>
629464b96c2e 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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81 <citation type="doi">doi.org/10.1038/s41587-020-0501-8</citation>
629464b96c2e 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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82 <citation type="doi">dx.doi.org/10.1038/nbt.4229</citation>
629464b96c2e 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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83 </citations>
629464b96c2e 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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84 </tool>