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comparison data_manager/genomad_datamanager.xml @ 0:74d51566155d draft default tip

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planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_genomad commit fea5692fe5258a520e43b739c5aa4d109756123f
author ufz
date Fri, 13 Jun 2025 20:39:57 +0000
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1 <?xml version="1.0"?>
2 <tool id="genomad_build_database" name="geNomad" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>database builder</description>
4 <macros>
5 <token name="@TOOL_VERSION@">1.11.1</token>
6 <token name="@VERSION_SUFFIX@">0</token>
7 <token name="@PROFILE@">22.01</token>
8 </macros>
9 <requirements>
10 <requirement type="package" version="1.21.4">wget</requirement>
11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[
13 set -eo pipefail;
14 wget -O -
15 ## #if $version == "test"
16 ## https://zenodo.org/records/11945948/files/genomad_microdb.tar.gz?download=1
17 ## #else
18 https://portal.nersc.gov/genomad/__data__/genomad_db_v${version}.tar.gz
19 ## alternatively https://zenodo.org/records/14886553, but constructing the links is more complicated
20 ## #end if
21 | tar -xzv &&
22 mkdir -p '$out_file.extra_files_path' &&
23 mv genomad_db '$out_file.extra_files_path' &&
24 cp '$dmjson' '$out_file'
25 ]]></command>
26 <configfiles>
27 <configfile name="dmjson"><![CDATA[
28 {
29 "data_tables":{
30 "genomad":[
31 {
32 "path":"genomad_db",
33 "name":"Version $version",
34 "value":"$version"
35 }
36 ]
37 }
38 }]]>
39 </configfile>
40 </configfiles>
41 <inputs>
42 <param name="version" type="select" multiple="false" label="Database Version" help="Download the chosen version from https://portal.nersc.gov/genomad/__data__/">
43 <option value="1.7">1.7</option>
44 <option value="1.9">1.9</option>
45 <!-- <option value="test">test</option> -->
46 </param>
47 </inputs>
48 <outputs>
49 <data name="out_file" format="data_manager_json" />
50 </outputs>
51 <tests>
52 <test expect_num_outputs="1">
53 <param name="version" value="1.9" />
54 <output name="out_file">
55 <assert_contents>
56 <has_text text='"value":"1.9"'/>
57 <has_text text='"name":"Version 1.9"'/>
58 </assert_contents>
59 </output>
60 </test>
61 </tests>
62 <help><![CDATA[
63 Download and extract geNomad database from https://portal.nersc.gov/genomad/__data__/
64
65 Check for tool and DB version compatibility here: https://portal.nersc.gov/genomad/__data__/releases.txt
66 ]]></help>
67 <citations>
68 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
69 </citations>
70 </tool>