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comparison data_manager/data_manager_build_amrfinderplus.xml @ 0:43ec3aadda50 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
author pimarin
date Tue, 20 Dec 2022 13:43:51 +0000
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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>
3 <macros>
4 <import>macro.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code">
8 <![CDATA[
9 python '$__tool_directory__/data_manager_build_amrfinderplus.py'
10 '$output_file'
11 --db_version '$database_list.database_version_select'
12 #if $database_list.database_version_select != 'latest':
13 --db_date '$database_list.database_date_select'
14 #end if
15 $test_data_manager
16 ]]></command>
17 <inputs>
18 <conditional name="database_list">
19 <param name="database_version_select" type="select" label="Database version">
20 <option value="latest" selected="true">Latest available version</option>
21 <option value="3.10">V3.10</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>
26 <when value="latest">
27 </when>
28 <when value="3.10">
29 <param name="database_date_select" type="select" label="Date version">
30 <option value="2022-10-11.2" selected="true">2022-10-11.2</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>
40 </when>
41 <when value="3.9">
42 <param name="database_date_select" type="select" label="Date version">
43 <option value="2020-11-09.1" selected="true">2020-11-09.1</option>
44 <option value="2020-12-17.1">2020-12-17.1</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>
61 </when>
62 </conditional>
63 <param name="test_data_manager" type="hidden" value=""/>
64 </inputs>
65 <outputs>
66 <data name="output_file" format="data_manager_json"/>
67 </outputs>
68 <tests>
69 <!-- Test_1 DB latest -->
70 <test expect_num_outputs="1">
71 <param name="test_data_manager" value="--test"/>
72 <output name="output_file" value="amrfinderplus_test_data_manager_1.json"/>
73 </test>
74 <!-- Test_2 DB 3.2 -->
75 <test expect_num_outputs="1">
76 <param name="test_data_manager" value="--test"/>
77 <conditional name="database_list">
78 <param name="database_version_select" value="3.6"/>
79 <param name="database_date_select" value="2020-03-20.1"/>
80 </conditional>
81 <output name="output_file" value="amrfinderplus_test_data_manager_2.json"/>
82 </test>
83
84
85 </tests>
86 <help><![CDATA[
87 Download amrfinderplus database from the NCBI server
88 ]]></help>
89 <citations>
90 <citation type="doi">10.1038/s41598-021-91456-0</citation>
91 </citations>
92 </tool>