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comparison data_manager/mitos_fetcher.xml @ 0:d1beb6fba192 draft default tip

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit a7354d02377105590891f7337f472dc2a2f224a4
author matthias
date Thu, 09 May 2019 16:20:33 -0400
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-1:000000000000 0:d1beb6fba192
1 <?xml version="1.0"?>
2 <tool id="mitos_fetcher_data_manager" name="MITOS" tool_type="manage_data" version="0.0.1">
3 <description>reference data downloader</description>
4 <command detect_errors="exit_code">
5 <![CDATA[
6 python '$__tool_directory__/data_manager.py'
7 --out '${out_file}'
8 --type '$type_cond.type_select'
9 --db '$type_cond.database'
10 ]]>
11 </command>
12 <inputs>
13 <conditional name="type_cond">
14 <param name="type_select" type="select" label="MITOS version">
15 <option value="mitos">MITOS</option>
16 <option value="mitos2">MITOS2</option>
17 </param>
18 <when value="mitos">
19 <param name="database" type="select" label="Refernce data version">
20 <option value="mitos1-refdata">RefSeq39 + MiTFi tRNA models</option>
21 </param>
22 </when>
23 <when value="mitos2">
24 <param name="database" type="select" label="Refernce data version">
25 <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option>
26 <option value="refseq63m">RefSeq63 Metazoa</option>
27 <option value="refseq63f">RefSeq63 Fungi</option>
28 <option value="refseq63o">RefSeq63 Opisthokonta</option>
29 <option value="refseq81m">RefSeq81 Metazoa</option>
30 <option value="refseq81f">RefSeq81 Fungi</option>
31 <option value="refseq81o">RefSeq81 Opisthokonta</option>
32 </param>
33 </when>
34 </conditional>
35 </inputs>
36 <outputs>
37 <data name="out_file" format="data_manager_json" />
38 </outputs>
39 <tests>
40 <test>
41 <conditional name="type_cond">
42 <param name="type_select" value="mitos"/>
43 <param name="database" value="mitos1-refdata"/>
44 </conditional>
45 <output name="out_file" file="mitos_refseq39.json"/>
46 </test>
47 </tests>
48 <help>
49 TODO
50 </help>
51 </tool>
52