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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
author frogs
date Mon, 23 Aug 2021 10:21:10 +0000
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1 <tool id="FROGS_data_manager" name="FROGS Data manager" version="3.2.3+galaxy2" tool_type="manage_data">
2 <requirements>
3 </requirements>
4 <stdio>
5 <exit_code range="1:" />
6 </stdio>
7 <command><![CDATA[
8 $__tool_directory__/FROGS_data_manager.py
9 --database="frogs_db_data"
10
11 --all_dbs="$db_type.db"
12 #if $db_type.db=="false"
13 --date="$db_type.date"
14 --amplicons="$db_type.amplicons"
15 --bases="$db_type.bases"
16 --filters="$db_type.filters"
17 #end if
18 --only_last_versions="$only_last_versions"
19
20 --tool_data="$__tool_data_path__"
21 --output "$output"
22 ]]></command>
23 <inputs>
24 <conditional name="db_type">
25 <param name="db" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Download all databases"/>
26 <when value="true"/>
27 <when value="false">
28 <param name="date" value="0" type="text" label="Download only most recent databases" help="Select databases uploaded later than this date. Please enter a date at the following format: YYYYMMDD, else leave 0.">
29 <validator type="regex" message="Please enter a date at the following format: YYYYMMDD, leave 0 for no date">0|[1-2]{1}[0-9]{3}[0-1]{1}[0-9]{1}([0-2]{1}[0-9]{1}|3[0-1]{1})</validator>
30 </param>
31 <param name="amplicons" type="text" label='Select amplicon specific databases' help='Write amplicons names separated by ","; example: "COI,ITS,16S" or "23S"'/>
32 <param name="bases" type="text" label='Select database by name' help='Write base names separated by ","; example: "SILVA,PR2,MIDAS" or "BOLD"'/>
33 <param name="filters" type="text" label='Select database on filter name' help='Write filter names separated by ",";example: "Pintail100,Fungi"'/>
34 </when>
35 </conditional>
36 <param name="only_last_versions" type="boolean" checked="true" label="Download only the last version of selected database"/>
37 </inputs>
38 <outputs>
39 <data name="output" format="data_manager_json"/>
40 </outputs>
41 <help>
42
43 .. image:: static/images/FROGS_logo.png
44 :height: 144
45 :width: 110
46
47 FROGS datamanager allows to download preformated databases for FROGS Affiliation OTU tool.
48
49 All databases are available at http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/.
50
51 This tools is based on the `FROGS_databases.tsv.txt &lt;http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/FROGS_databases.tsv&gt;`_, that we update each time a new database is formatted.
52
53 .. image:: static/images/FROGS_db.png
54 :height: 157
55 :width: 961
56
57 You may download all databases, but you may (should) filter whished database on different criteria:
58
59 - on a date, to download only last formated databases
60 - on an amplicon type
61 - on a base name
62 - eventually on a filtered name, this may be the case for example, for 16S SILVA database, for which we provide reference sequence with pintail score above a threshold
63
64 Last option allow you to download only last version of previously selected databases, indeed we provide reference database since 2016 with for example, around 1 version of SILVA per year.
65
66 **Contact**
67
68 Contacts: frogs-support@inrae.fr
69
70 Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
71
72 Website: http://frogs.toulouse.inrae.fr/
73
74 </help>
75 </tool>