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comparison data_manager/data_manager_mitos.xml @ 0:26a6f95e82c8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
author iuc
date Fri, 27 Mar 2020 17:50:23 -0400
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children 19d9be08560c
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1 <?xml version="1.0"?>
2 <tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.1">
3 <description>reference data downloader</description>
4 <requirements>
5 <requirement type="package" version="3.7">python</requirement>
6 </requirements>
7 <command detect_errors="exit_code">
8 <![CDATA[
9 python '$__tool_directory__/data_manager.py'
10 --out '${out_file}'
11 --type '$type_cond.type_select'
12 --db '$type_cond.database'
13 ]]>
14 </command>
15 <inputs>
16 <conditional name="type_cond">
17 <param name="type_select" type="select" label="MITOS version">
18 <option value="mitos">MITOS</option>
19 <option value="mitos2">MITOS2</option>
20 </param>
21 <when value="mitos">
22 <param name="database" type="select" label="Reference data version">
23 <option value="mitos1-refdata">RefSeq39 + MiTFi tRNA models</option>
24 </param>
25 </when>
26 <when value="mitos2">
27 <param name="database" type="select" label="Reference data version">
28 <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option>
29 <option value="refseq63m">RefSeq63 Metazoa</option>
30 <option value="refseq63f">RefSeq63 Fungi</option>
31 <option value="refseq63o">RefSeq63 Opisthokonta</option>
32 <option value="refseq89m">RefSeq89 Metazoa</option>
33 <option value="refseq89f">RefSeq89 Fungi</option>
34 <option value="refseq89o">RefSeq89 Opisthokonta</option>
35 </param>
36 </when>
37 </conditional>
38 </inputs>
39 <outputs>
40 <data name="out_file" format="data_manager_json" />
41 </outputs>
42 <tests>
43 <test>
44 <conditional name="type_cond">
45 <param name="type_select" value="mitos"/>
46 <param name="database" value="mitos1-refdata"/>
47 </conditional>
48 <output name="out_file" file="mitos_refseq39.json"/>
49 </test>
50 </tests>
51 <help>
52 This data manager downloads MITOS and MITOS2 reference data for use in Galaxy.
53
54 For MITOS the reference data includes
55
56 - protein data bases derived from RefSeq release 39 (see Bernt et al. 2012)
57 - covariance models for tRNAs and rRNAs as described in Jühling et al 2012
58
59 Data is downloaded from https://zenodo.org/record/2683856.
60
61 For MITOS2 the reference data sets are available for three different taxons
62
63 - Metazoa
64 - Fungi
65 - Opisthokonta
66
67 these have been computed for RefSeq release 63 and 89. In addition the reference data
68 for MITOS1 has been converted to be usable in MITOS2.
69 contains
70
71 The reference data sets contain:
72
73 - protein data bases derived from the corresponding RefSeq release Donath et al. 2019
74 - covariance models computed for the data in the RefSeq releas based on the MITOS1 models
75 - in addition for Metazoa Release 63 also hidden markov models are available as described in Al Arab et al. 2017
76
77 Data is downloaded from https://zenodo.org/record/3685310.
78 </help>
79 <citations>
80 <citation type="doi">10.1016/j.ympev.2012.08.023</citation>
81 <citation type="doi">10.1093/nar/gkr1131</citation>
82 <citation type="doi">10.1016/j.ympev.2016.09.024</citation>
83 <citation type="doi">10.1093/nar/gkz833</citation>
84 </citations>
85 </tool>
86