Mercurial > repos > galaxytrakr > data_manager_mapseq

comparison data_manager/data_manager_mapseq.xml @ 2:b2591ceb5ec2 draft

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planemo upload commit 960e71a63820069f2022e7b146a0f2118cb47d45
author galaxytrakr
date Thu, 26 Mar 2026 20:40:41 +0000
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children 472239da4582
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1:97634e034eed 2:b2591ceb5ec2
1 <tool id="mapseq_db_fetcher" name="Mapseq DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Fetches the DB required for mapseq</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version" />
8 <command detect_errors="exit_code">
9 <![CDATA[
10 python '$__tool_directory__/data_manager_fetch_mapseq_db.py'
11 --out '${out_file}'
12 --version '${select_version.version}'
13 --database-type '${database_type}'
14 ]]>
15 </command>
16 <inputs>
17 <conditional name="select_version">
18 <param argument="--version" type="select" label="Select MGnify version">
19 <option value="5.0">v5.0</option>
20 <option value="6.0">v6.0</option>
21 </param>
22 <when value="5.0">
23 <param name="database_type" type="select" multiple="false" label="Database Type">
24 <option value="mgnify_v5_lsu">MGnify LSU (v5.0.7)</option>
25 <option value="mgnify_v5_ssu">MGnify SSU (v5.0.7)</option>
26 <option value="mgnify_v5_its_itsonedb">MGnify ITS ITSonedb (v5.0.7)</option>
27 <option value="mgnify_v5_its_unite">MGnify ITS UNITE (v5.0.7)</option>
28 </param>
29 </when>
30 <when value="6.0">
31 <param name="database_type" type="select" multiple="false" label="Database Type">
32 <option value="mgnify_v6_lsu">MGnify LSU (v6.0)</option>
33 <option value="mgnify_v6_ssu">MGnify SSU (v6.0)</option>
34 <option value="mgnify_v6_its_itsonedb">MGnify ITS ITSonedb (v6.0)</option>
35 <option value="mgnify_v6_its_unite">MGnify ITS UNITE (v6.0)</option>
36 <option value="mgnify_v6_pr2">MGnify PR2 (v6.0)</option>
37 </param>
38 </when>
39 </conditional>
40 </inputs>
41 <outputs>
42 <data format="data_manager_json" name="out_file" />
43 </outputs>
44 <tests>
45 </tests>
46 <help>
47 Downloads preformatted DBs form MGnify that can be used for mapseq.
48 The download paths were taken from: https://github.com/EBI-Metagenomics/pipeline-v5/
49 </help>
50 <expand macro="citations" />
51 <expand macro="creator" />
52 </tool>