Mercurial > repos > iuc > data_manager_gtdbtk_database_installer
comparison data_manager/gtdbtk_database_installer.xml @ 7:3b1d503c6260 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 671e8c706fa211b6ec1c476d3d1a36d098822fe5
author | iuc |
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date | Thu, 03 Oct 2024 12:42:22 +0000 |
parents | df84aaed4769 |
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6:df84aaed4769 | 7:3b1d503c6260 |
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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@"> | 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> | 2 <description></description> |
3 <macros> | 3 <macros> |
4 <token name="@TOOL_VERSION@">202</token> | 4 <token name="@TOOL_VERSION@">202</token> |
5 <token name="@VERSION_SUFFIX@">2</token> | 5 <token name="@VERSION_SUFFIX@">3</token> |
6 <token name="@PROFILE@">20.09</token> | 6 <token name="@PROFILE@">20.09</token> |
7 </macros> | 7 </macros> |
8 <requirements> | 8 <requirements> |
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_name '$database_name' | 14 --release '$release' |
15 --release '$release' | 15 --out_file '$out_file' |
16 --out_file '$out_file' | 16 $meta |
17 $meta | 17 $test |
18 $test | |
19 ]]> | 18 ]]> |
20 </command> | 19 </command> |
21 <inputs> | 20 <inputs> |
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"/> | 21 <param name="meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Only store GTDBTK metadata in a dedicated data table. " /> |
23 <param name="meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Only store GTDBTK metadata in a dedicated data table. " /> | 22 <param name="test" type="hidden" value="" checked="false" label="Run a dry test run!" /> |
24 <param name="test" type="hidden" value="" checked="false" label="Run a dry test run !" /> | |
25 <param name="release" type="select" multiple="false" label="GTDB Release"> | 23 <param name="release" type="select" multiple="false" label="GTDB Release"> |
26 <option value="202">202</option> | 24 <option value="202">202</option> |
27 <option value="207">207</option> | 25 <option value="207">207</option> |
28 <option value="214">214</option> | 26 <option value="214">214</option> |
29 <option value="220">220</option> | 27 <option value="220">220</option> |
32 <outputs> | 30 <outputs> |
33 <data name="out_file" format="data_manager_json"/> | 31 <data name="out_file" format="data_manager_json"/> |
34 </outputs> | 32 </outputs> |
35 <tests> | 33 <tests> |
36 <test> | 34 <test> |
37 <!-- TODO --> | |
38 <!-- Not actually installing a huge GTDB-Tk database --> | 35 <!-- Not actually installing a huge GTDB-Tk database --> |
39 <!-- but it will check if all urls exist --> | 36 <!-- but it will check if all urls exist --> |
40 <param name="release" value="202"/> | 37 <param name="release" value="202"/> |
41 <param name="database_name" value="GTDB-Tk database release 202"/> | |
42 <param name="test" value="--test"/> | 38 <param name="test" value="--test"/> |
43 <output name="out_file"> | 39 <output name="out_file"> |
44 <assert_contents> | 40 <assert_contents> |
45 <has_text text="GTDB-Tk database release 202"/> | 41 <has_text text="Full Database - release 202 "/> |
46 <has_text text="release_202"/> | 42 <has_text text="full_database_release_202_downloaded"/> |
47 </assert_contents> | 43 </assert_contents> |
48 </output> | 44 </output> |
49 </test> | 45 </test> |
50 <test> | 46 <test> |
51 <!-- Test meta data download with tsv.gz--> | 47 <!-- Test meta data download with tsv.gz--> |
52 <param name="release" value="220"/> | 48 <param name="release" value="220"/> |
53 <param name="database_name" value="GTDB-Tk database release 220 metadata"/> | |
54 <param name="meta" value="true"/> | 49 <param name="meta" value="true"/> |
55 <output name="out_file"> | 50 <output name="out_file"> |
56 <assert_contents> | 51 <assert_contents> |
57 <has_text text="GTDB-Tk database release 220 metadata"/> | 52 <has_text text="Metadata Tables - release 220"/> |
58 <has_text text="release_220"/> | 53 <has_text text="metadata_tables_release_220_downloaded_"/> |
59 </assert_contents> | 54 </assert_contents> |
60 </output> | 55 </output> |
61 </test> | 56 </test> |
62 <test> | 57 <test> |
63 <!-- Test meta data download with tar.gz --> | 58 <!-- Test meta data download with tar.gz --> |
64 <param name="release" value="207"/> | 59 <param name="release" value="207"/> |
65 <param name="database_name" value="GTDB-Tk database release 207 metadata"/> | |
66 <param name="meta" value="true"/> | 60 <param name="meta" value="true"/> |
67 <output name="out_file"> | 61 <output name="out_file"> |
68 <assert_contents> | 62 <assert_contents> |
69 <has_text text="GTDB-Tk database release 207 metadata"/> | 63 <has_text text="Metadata Tables - release 207"/> |
70 <has_text text="release_207"/> | 64 <has_text text="metadata_tables_release_207_downloaded_"/> |
71 </assert_contents> | 65 </assert_contents> |
72 </output> | 66 </output> |
73 </test> | 67 </test> |
74 </tests> | 68 </tests> |
75 <help> | 69 <help> |