Mercurial > repos > greg > data_manager_gtdbtk_database_installer

comparison data_manager/gtdbtk_database_installer.xml @ 0:3ab83cb7e2d2 draft

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author greg
date Tue, 15 Mar 2022 15:32:31 +0000
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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@">
2 <description></description>
3 <macros>
4 <token name="@TOOL_VERSION@">202</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 <token name="@PROFILE@">20.09</token>
7 </macros>
8 <requirements>
9 <requirement type="package" version="3.10.2">python</requirement>
10 </requirements>
11 <command>
12 <![CDATA[
13 python '$__tool_directory__/gtdbtk_database_installer.py'
14 --database_id '$database_id'
15 --database_name '$database_name'
16 --url '$url'
17 --out_file '$out_file'
18 ]]>
19 </command>
20 <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_id" type="text" value="" label="Database id" help="This value must be unique with nNo whitespace allowed-use underscores"/>
23 <param name="url" type="text" value="https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_data.tar.gz" label="URL for downloading the selected version of the GTDB-Tk database"/>
24 </inputs>
25 <outputs>
26 <data name="out_file" format="data_manager_json" />
27 </outputs>
28 <tests>
29 <test>
30 <!-- Not actually installing a huge GTDB-Tk database -->
31 <param name="database_id" value="release202"/>
32 <param name="database_name" value="GTDB-Tk database release 202"/>
33 <param name="url" value="https://data.gtdb.ecogenomic.org/releases/release202/202.0/VERSION"/>
34 <output name="out_file">
35 <assert_contents>
36 <has_text text="GTDB-Tk database release 202"/>
37 <has_text text="release202"/>
38 </assert_contents>
39 </output>
40 </test>
41 </tests>
42 <help>
43 </help>
44 <citations>
45 <citation type="doi">doi.org/10.1038/s41587-020-0501-8</citation>
46 <citation type="doi">dx.doi.org/10.1038/nbt.4229</citation>
47 </citations>
48 </tool>