diff data_manager/FROGS_data_manager.xml @ 0:493202ba3af5 draft

"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 56a8d94cd18a5b89f83ccfa9cdc7c80a28d044d4-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/FROGS_data_manager.xml	Wed Aug 18 15:24:49 2021 +0000
@@ -0,0 +1,64 @@
+<tool id="FROGS_data_manager" name="FROGS Data manager" version="3.2.2" tool_type="manage_data">
+    <requirements>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        $__tool_directory__/FROGS_data_manager.py
+            --database="frogs_db_data"
+            
+            --all_dbs="$db_type.db"
+            #if $db_type.db=="false"
+                --date="$db_type.date"
+                --amplicons="$db_type.amplicons"
+                --bases="$db_type.bases"
+                --filters="$db_type.filters"
+            #end if
+            --only_last_versions="$only_last_versions"
+            
+            --tool_data="$__tool_data_path__"
+            --output "$output"
+    ]]></command>
+    <inputs>
+        <conditional name="db_type">
+            <param name="db" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Download all databases"/>
+            <when value="true"/>
+            <when value="false">
+                <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.">
+                    <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>
+                </param>
+                <param name="amplicons" type="text" label='Select amplicon specific databases' help='Write amplicons names separated by ","; example: "COI,ITS,16S" or "23S"'/>
+                <param name="bases" type="text" label='Select database by name' help='Write base names separated by ","; example: "SILVA,PR2,MIDAS" or "BOLD"'/>
+                <param name="filters" type="text" label='Select database on filter name' help='Write filter names separated by ",";example: "Pintail100,Fungi"'/>
+            </when>
+        </conditional>
+        <param name="only_last_versions" type="boolean" checked="true" label="Download only the last version of selected database"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="data_manager_json"/>
+    </outputs>
+    <help>
+        
+       	@HELP_LOGO@
+
+        FROGS datamanager allows to download preformated databases for FROGS Affiliation OTU tool.
+
+        All databases are available at http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/.
+        
+        This tools is based on the `FROGS_databases.tsv.txt &lt;http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/FROGS_databases.tsv.txt&gt;`_, that we update each time a new database is formatted.
+
+		.. image:: static/images/FROGS_db.png
+   			:height: 157
+   			:width: 961
+
+   		You may download all databases, but you may (should) filter whished database on different criteria:
+
+   		- on a date, to download only last formated databases
+   		- on an amplicon type
+   		- on a base name
+   		- 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
+
+   		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.
+    </help>
+</tool>
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