Mercurial > repos > oinizan > data_manager_frogs

annotate data_manager/FROGS_data_manager.xml @ 4:34192d63196e draft default tip

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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 052af90b7eee0ccaff79e64e4706a8fbdb235783-dirty"
author oinizan
date Thu, 19 Aug 2021 14:53:38 +0000
parents 2d2f8d990bff
children
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1 <tool id="FROGS_data_manager" name="FROGS Data manager" version="3.2.3+galaxy2" tool_type="manage_data">
0
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2 <requirements>
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3 </requirements>
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4 <stdio>
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5 <exit_code range="1:" />
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6 </stdio>
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7 <command><![CDATA[
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8 $__tool_directory__/FROGS_data_manager.py
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9 --database="frogs_db_data"
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10
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11 --all_dbs="$db_type.db"
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12 #if $db_type.db=="false"
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13 --date="$db_type.date"
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14 --amplicons="$db_type.amplicons"
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15 --bases="$db_type.bases"
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16 --filters="$db_type.filters"
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17 #end if
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18 --only_last_versions="$only_last_versions"
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19
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20 --tool_data="$__tool_data_path__"
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21 --output "$output"
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22 ]]></command>
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23 <inputs>
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24 <conditional name="db_type">
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25 <param name="db" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Download all databases"/>
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26 <when value="true"/>
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27 <when value="false">
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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.">
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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>
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30 </param>
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31 <param name="amplicons" type="text" label='Select amplicon specific databases' help='Write amplicons names separated by ","; example: "COI,ITS,16S" or "23S"'/>
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32 <param name="bases" type="text" label='Select database by name' help='Write base names separated by ","; example: "SILVA,PR2,MIDAS" or "BOLD"'/>
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33 <param name="filters" type="text" label='Select database on filter name' help='Write filter names separated by ",";example: "Pintail100,Fungi"'/>
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34 </when>
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35 </conditional>
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36 <param name="only_last_versions" type="boolean" checked="true" label="Download only the last version of selected database"/>
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37 </inputs>
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38 <outputs>
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39 <data name="output" format="data_manager_json"/>
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40 </outputs>
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41 <help>
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42
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43 .. image:: static/images/FROGS_logo.png
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44 :height: 144
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45 :width: 110
0
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46
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47 FROGS datamanager allows to download preformated databases for FROGS Affiliation OTU tool.
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48
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49 All databases are available at http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/.
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50
1
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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.
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52
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53 .. image:: static/images/FROGS_db.png
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54 :height: 157
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55 :width: 961
0
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56
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57 You may download all databases, but you may (should) filter whished database on different criteria:
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58
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59 - on a date, to download only last formated databases
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60 - on an amplicon type
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61 - on a base name
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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
0
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63
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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.
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65
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66 **Contact**
0
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67
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68 Contacts: frogs-support@inrae.fr
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69
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70 Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
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71
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72 Website: http://frogs.toulouse.inrae.fr/
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73
0
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74 </help>
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75 </tool>