Mercurial > repos > iuc > amrfinderplus_data_manager_build

comparison data_manager/data_manager_build_amrfinderplus.xml @ 2:8fa7efc32500 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43
author iuc
date Sun, 23 Nov 2025 12:21:18 +0000
parents d4e3b8d47f49
children
comparison
equal deleted inserted replaced
1:d4e3b8d47f49 2:8fa7efc32500
1 <tool id="data_manager_build_amrfinderplus" name="amrfinderplus_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="data_manager_build_amrfinderplus" name="amrfinderplus_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>AMRfinderplus database builder</description> 2 <description>AMRFinderPlus database builder</description>
3 <macros> 3 <macros>
4 <import>macro.xml</import> 4 <import>macro.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
8 <![CDATA[ 8 <![CDATA[
9 python '$__tool_directory__/data_manager_build_amrfinderplus.py' 9 python '$__tool_directory__/data_manager_build_amrfinderplus.py'
10 '$output_file' 10 '$output_file'
11 --db_version '$database_list.database_version_select' 11 --db_version '$database_list.database_version_select'
12 #if $database_list.database_version_select != 'latest': 12 #if $database_list.database_version_select != 'latest':
13 --db_date '$database_list.database_date_select' 13 --db_date '$database_list.database_date_select'
14 #end if 14 #end if
15 $test_data_manager 15 $test_data_manager
16 ]]></command> 16 ]]></command>
17 <inputs> 17 <inputs>
18 <conditional name="database_list"> 18 <conditional name="database_list">
19 <param name="database_version_select" type="select" label="Database version"> 19 <param name="database_version_select" type="select" label="Database version">
20 <option value="latest" selected="true">Latest available version</option> 20 <option value="4.0">V4.0</option>
21 <option value="3.10">V3.10</option> 21 <option value="3.12">V3.12</option>
22 <option value="3.9">V3.9</option>
23 <option value="3.8">V3.8</option>
24 <option value="3.6">V3.6</option>
25 </param> 22 </param>
26 <when value="latest"> 23 <when value="4.0">
27 </when>
28 <when value="3.10">
29 <param name="database_date_select" type="select" label="Date version"> 24 <param name="database_date_select" type="select" label="Date version">
30 <option value="2022-10-11.2" selected="true">2022-10-11.2</option> 25 <option value="2025-07-16.1">2025-07-16.1</option>
31 <option value="2022-08-09.1">2022-08-09.1</option>
32 <option value="2022-05-26.1">2022-05-26.1</option>
33 <option value="2022-04-04.1">2022-04-04.1</option>
34 <option value="2021-12-21.1">2021-12-21.1</option>
35 <option value="2021-09-30.1">2021-09-30.1</option>
36 <option value="2021-09-30.1">2021-08-11.1</option>
37 <option value="2021-09-30.1">2021-06-01.1</option>
38 <option value="2021-09-30.1">2021-03-01.1</option>
39 </param> 26 </param>
40 </when> 27 </when>
41 <when value="3.9"> 28 <when value="3.12">
42 <param name="database_date_select" type="select" label="Date version"> 29 <param name="database_date_select" type="select" label="Date version">
43 <option value="2020-11-09.1" selected="true">2020-11-09.1</option> 30 <option value="2024-05-02.2">2024-05-02.2</option>
44 <option value="2020-12-17.1">2020-12-17.1</option> 31 <option value="2024-01-31.1">2024-01-31.1</option>
45 </param>
46 </when>
47 <when value="3.8">
48 <param name="database_date_select" type="select" label="Date version">
49 <option value="2020-09-30.1" selected="true">2020-09-30.1</option>
50 <option value="2020-09-22.2">2020-09-22.2</option>
51 <option value="2020-07-16.2">2020-07-16.2</option>
52 <option value="2020-06-11.1">2020-06-11.1</option>
53 <option value="2020-05-04.1">2020-05-04.1</option>
54 </param>
55 </when>
56 <when value="3.6">
57 <param name="database_date_select" type="select" label="Date version">
58 <option value="2020-01-22.1" selected="true">2020-01-22.1</option>
59 <option value="2020-03-20.1">2020-03-20.1</option>
60 </param> 32 </param>
61 </when> 33 </when>
62 </conditional> 34 </conditional>
63 <param name="test_data_manager" type="hidden" value=""/> 35 <param name="test_data_manager" type="hidden" value=""/>
64 </inputs> 36 </inputs>
65 <outputs> 37 <outputs>
66 <data name="output_file" format="data_manager_json"/> 38 <data name="output_file" format="data_manager_json"/>
67 </outputs> 39 </outputs>
68 <tests> 40 <tests>
71 <param name="test_data_manager" value="--test"/> 43 <param name="test_data_manager" value="--test"/>
72 <output name="output_file"> 44 <output name="output_file">
73 <assert_contents> 45 <assert_contents>
74 <has_n_lines n="1"/> 46 <has_n_lines n="1"/>
75 <has_text text="{&quot;data_tables&quot;"/> 47 <has_text text="{&quot;data_tables&quot;"/>
76 <has_text text="amrfinderplus_database"/> 48 <has_text text="amrfinderplus_versioned_database"/>
77 </assert_contents> 49 </assert_contents>
78 </output> 50 </output>
79 </test> 51 </test>
80 <!-- Test_2 DB 3.2 --> 52 <!-- Test_2 DB 3.12 2024-01-31.1 -->
81 <test expect_num_outputs="1"> 53 <test expect_num_outputs="1">
82 <param name="test_data_manager" value="--test"/> 54 <param name="test_data_manager" value="--test"/>
83 <conditional name="database_list"> 55 <conditional name="database_list">
84 <param name="database_version_select" value="3.6"/> 56 <param name="database_version_select" value="3.12"/>
85 <param name="database_date_select" value="2020-03-20.1"/> 57 <param name="database_date_select" value="2024-01-31.1"/>
86 </conditional> 58 </conditional>
87 <output name="output_file" value="amrfinderplus_test_data_manager_2.json"/> 59 <output name="output_file">
60 <assert_contents>
61 <has_n_lines n="1"/>
62 <has_text text="{&quot;data_tables&quot;"/>
63 <has_text text="amrfinderplus_versioned_database"/>
64 <has_text text='"name": "V3.12-2024-01-31.1"'/>
65 <has_text text='"db_version": "3.12"'/>
66 </assert_contents>
67 </output>
88 </test> 68 </test>
89 69 <!-- Test_3 DB 4.0 2025-07-16.1 -->
90 70 <test expect_num_outputs="1">
71 <param name="test_data_manager" value="--test"/>
72 <conditional name="database_list">
73 <param name="database_version_select" value="4.0"/>
74 <param name="database_date_select" value="2025-07-16.1"/>
75 </conditional>
76 <output name="output_file">
77 <assert_contents>
78 <has_n_lines n="1"/>
79 <has_text text="{&quot;data_tables&quot;"/>
80 <has_text text="amrfinderplus_versioned_database"/>
81 <has_text text='"name": "V4.0-2025-07-16.1"'/>
82 <has_text text='"db_version": "4.0"'/>
83 </assert_contents>
84 </output>
85 </test>
91 </tests> 86 </tests>
92 <help><![CDATA[ 87 <help><![CDATA[
93 Download amrfinderplus database from the NCBI server 88 Download AMRFinderPlus database from the NCBI server
94 ]]></help> 89 ]]></help>
95 <citations> 90 <citations>
96 <citation type="doi">10.1038/s41598-021-91456-0</citation> 91 <citation type="doi">10.1038/s41598-021-91456-0</citation>
97 </citations> 92 </citations>
98 </tool> 93 </tool>