|
0
|
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>
|
|
1
|
26 <data name="out_file" format="data_manager_json"/>
|
|
0
|
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>
|
