Mercurial > repos > iuc > data_manager_qiime_database_downloader

comparison data_manager/data_manager_qiime_download.xml @ 0:f8608fddfb23 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
author iuc
date Mon, 15 May 2017 11:08:43 -0400
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children cbe065fbd038
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-1:000000000000 0:f8608fddfb23
1 <tool id="data_manager_qiime_download" name="Download QIIME" version="1.9.1" tool_type="manage_data">
2 <description>reference databases</description>
3 <requirements>
4 <requirement type="package" version="2.13.0">requests</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
8 <exit_code range="1:" level="fatal" description="Error" />
9 </stdio>
10 <command><![CDATA[
11 python '$__tool_directory__/data_manager_qiime_download.py'
12 --database '$db.database'
13 --version '$db.version'
14 --jsonfile '${out_file}'
15 ]]></command>
16 <inputs>
17 <conditional name="db">
18 <param name="database" type="select" label="Database to download">
19 <option value="greengenes" selected="true">Greengenes OTUs</option>
20 <option value="silva">SILVA OTUs (16S/18S)</option>
21 <option value="unite">UNITE OTUs (ITS)</option>
22 <!--<option value="img">IMG/QIIME reference protein sequences</option>-->
23 </param>
24 <when value="greengenes">
25 <param name="version" type="select" label="Version of Greengenes">
26 <option value="13_8" selected="true">13.8</option>
27 <option value="13_5">13.5</option>
28 <option value="12_10">12.10</option>
29 </param>
30 </when>
31 <when value="silva">
32 <param name="version" type="select" label="Version of SILVA OTUs">
33 <option value="128_release" selected="true">128</option>
34 <option value="123_release">123</option>
35 <!--<option value="119_release_aligned_rep_files">119 (aligned rep)</option>
36 <option value="119_release">119</option>
37 <option value="119_consensus_majority_taxonomy">119 (consensus majority taxonomy)</option>
38 <option value="111_release">111</option>
39 <option value="108_release">108</option>
40 <option value="108_release_curated">108 (curated)</option>
41 <option value="104_release">104</option>-->
42 </param>
43 </when>
44 <when value="unite">
45 <param name="version" type="select" label="Version of UNITE OTUs">
46 <option value="20.11.2016">7.1 (2016-11-20, with singletons set as RefS)</option>
47 <option value="s_20.11.2016">7.1 (2016-11-20, with global and 97% singletons)</option>
48 <option value="22.08.2016">7.1 (2016-08-22, with singletons set as RefS)</option>
49 <option value="s_22.08.2016">7.1 (2016-08-22, with global and 97% singletons)</option>
50 <option value="31.01.2016">7.0 (2016-01-31, with singletons set as RefS)</option>
51 <option value="s_31.01.2016">7.0 (2016-01-31, with global and 97% singletons)</option>
52 <option value="01.08.2015">7.0 (2015-08-01, with singletons set as RefS)</option>
53 <option value="s_01.08.2015">7.0 (2015-08-01, with global and 97% singletons)</option>
54 <option value="02.03.2015">7.0 (2015-03-02, with singletons set as RefS)</option>
55 <option value="s_02.03.2015">7.0 (2015-03-02, with global and 97% singletons)</option>
56 <option value="30.12.2014">6.0 (2014-12-30, with singletons set as RefS)</option>
57 <option value="s_30.12.2014">6.0 (2014-12-30, with global and 97% singletons)</option>
58 <option value="10.09.2014">6.0 (2014-09-10, with singletons set as RefS)</option>
59 <option value="s_10.09.2014">6.0 (2014-09-10, with global and 97% singletons)</option>
60 <option value="04.07.2014">6.0 (2014-07-04, with singletons set as RefS)</option>
61 <option value="s_04.07.2014">6.0 (2014-07-04, with global and 97% singletons)</option>
62 <option value="13.05.2014">6.0 (2014-05-13, with singletons set as RefS)</option>
63 <option value="s_13.05.2014">6.0 (2014-05-13, with global and 97% singletons)</option>
64 <option value="09.02.2014">6.0 (2014-02-09, with singletons set as RefS)</option>
65 <option value="s_09.02.2014">6.0 (2014-02-09, with global and 97% singletons)</option>
66 <option value="15.01.2014">6.0 (2014-01-15, with singletons set as RefS)</option>
67 <option value="s_15.01.2014">6.0 (2014-01-15, with global and 97% singletons)</option>
68 <option value="19.12.2013">6.0 (2013-12-19, with singletons set as RefS)</option>
69 <option value="s_19.12.2013">6.0 (2013-12-19, with global and 97% singletons)</option>
70 <option value="08.12.2013">6.0 (2013-12-08, with singletons set as RefS)</option>
71 <option value="s_08.12.2013">6.0 (2013-12-08, with global and 97% singletons)</option>
72 <option value="15.10.2013">5.0 (2013-10-15, with singletons set as RefS)</option>
73 <option value="s_15.10.2013">5.0 (2013-10-15, with global and 97% singletons)</option>
74 </param>
75 </when>
76 <!--<when value="img">
77 <param name="version" type="select" label="Version of IMG/QIIME reference protein sequences">
78 <option value="img-qiime-25oct2012" selected="true">img-qiime-25oct2012</option>
79 </param>
80 </when>-->
81 </conditional>
82 </inputs>
83 <outputs>
84 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
85 </outputs>
86 <tests>
87 </tests>
88 <help><![CDATA[
89 This tool downloads the reference databases for QIIME
90 ]]></help>
91 <citations>
92 <citation type="doi">10.1038/nmeth.f.303</citation>
93 <yield />
94 </citations>
95 </tool>