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comparison data_manager/gtdbtk_database_installer.xml @ 2:9dcb593e8a43 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 ad14947c3e13babe90a6878b45608fe56a16150d
author iuc
date Tue, 13 Aug 2024 21:13:34 +0000
parents f54abc2f5707
children 700c4fbdd3e1
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1:f54abc2f5707 2:9dcb593e8a43
9 <requirement type="package" version="3.10.2">python</requirement> 9 <requirement type="package" version="3.10.2">python</requirement>
10 </requirements> 10 </requirements>
11 <command> 11 <command>
12 <![CDATA[ 12 <![CDATA[
13 python '$__tool_directory__/gtdbtk_database_installer.py' 13 python '$__tool_directory__/gtdbtk_database_installer.py'
14 --database_id '$database_id'
15 --database_name '$database_name' 14 --database_name '$database_name'
16 --url '$url' 15 --release '$release'
17 --out_file '$out_file' 16 --out_file '$out_file'
17 $meta
18 $test
18 ]]> 19 ]]>
19 </command> 20 </command>
20 <inputs> 21 <inputs>
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"/> 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"/>
22 <param name="database_id" type="text" value="" label="Database id" help="This value must be unique with no whitespace allowed - use underscores"/> 23 <param name="meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Only store GTDBTK metadata in a dedicated data table. " />
23 <param 24 <param name="test" type="hidden" value="" checked="false" label="Run a dry test run !" />
24 name="url" 25 <param name="release" type="select" multiple="false" label="GTDB Release">
25 type="text" 26 <option value="202">202</option>
26 value="https://data.gtdb.ecogenomic.org/releases/release202/202.0/auxillary_files/gtdbtk_r202_data.tar.gz" 27 <option value="207">207</option>
27 label="URL for GTDB release" 28 <option value="214">214</option>
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." 29 <option value="220">220</option>
29 /> 30 </param>
30 </inputs> 31 </inputs>
31 <outputs> 32 <outputs>
32 <data name="out_file" format="data_manager_json"/> 33 <data name="out_file" format="data_manager_json"/>
33 </outputs> 34 </outputs>
34 <tests> 35 <tests>
35 <test> 36 <test>
37 <!-- TODO -->
36 <!-- Not actually installing a huge GTDB-Tk database --> 38 <!-- Not actually installing a huge GTDB-Tk database -->
37 <param name="database_id" value="release202"/> 39 <param name="release" value="202"/>
38 <param name="database_name" value="GTDB-Tk database release 202"/> 40 <param name="database_name" value="GTDB-Tk database release 202"/>
39 <param name="url" value="https://data.gtdb.ecogenomic.org/releases/release202/202.0/VERSION"/> 41 <param name="test" value="--test"/>
40 <output name="out_file"> 42 <output name="out_file">
41 <assert_contents> 43 <assert_contents>
42 <has_text text="GTDB-Tk database release 202"/> 44 <has_text text="GTDB-Tk database release 202"/>
43 <has_text text="release202"/> 45 <has_text text="release_test"/>
46 </assert_contents>
47 </output>
48 </test>
49 <test>
50 <!-- Test meta data download -->
51 <param name="release" value="202"/>
52 <param name="database_name" value="GTDB-Tk database release 202 metadata"/>
53 <param name="meta" value="true"/>
54 <param name="test" value="--test"/>
55 <output name="out_file">
56 <assert_contents>
57 <has_text text="GTDB-Tk database release 202 metadata"/>
58 <has_text text="release_test"/>
44 </assert_contents> 59 </assert_contents>
45 </output> 60 </output>
46 </test> 61 </test>
47 </tests> 62 </tests>
48 <help> 63 <help>
64 This data manager downloads the DB required for GTDB-Tk tools such as
65 the `gtdbtk classify_wf`. The meta options allows downloading only the metadata for the
66 corresponding DB, which is used by tools like `gtdb_to_taxdump`.
49 </help> 67 </help>
50 <citations> 68 <citations>
51 <citation type="doi">doi.org/10.1038/s41587-020-0501-8</citation> 69 <citation type="doi">doi.org/10.1038/s41587-020-0501-8</citation>
52 <citation type="doi">dx.doi.org/10.1038/nbt.4229</citation> 70 <citation type="doi">dx.doi.org/10.1038/nbt.4229</citation>
53 </citations> 71 </citations>