Mercurial > repos > matthias > data_manager_mitos
comparison data_manager/mitos_fetcher.xml @ 0:d1beb6fba192 draft default tip
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit a7354d02377105590891f7337f472dc2a2f224a4
author | matthias |
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date | Thu, 09 May 2019 16:20:33 -0400 |
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-1:000000000000 | 0:d1beb6fba192 |
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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 |