Merge branch 'dev'

geraldinepascal · Apr 8, 2021 · e71bbd9 · e71bbd9
2 parents 3247067 + 4ba0594
commit e71bbd9
Showing 1 changed file with 25 additions and 7 deletions.
diff --git a/FROGS_data_manager/data_manager/FROGS_data_manager.xml b/FROGS_data_manager/data_manager/FROGS_data_manager.xml
@@ -1,4 +1,4 @@
-<tool id="FROGS_data_manager" name="FROGS Data manager" version="3.2.1" tool_type="manage_data">
+<tool id="FROGS_data_manager" name="FROGS Data manager" version="3.2.2" tool_type="manage_data">
     <requirements>
     </requirements>
     <stdio>
@@ -25,23 +25,41 @@
             <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="Only more recent database than this date will be downloaded" help="Please enter a date at the following format: YYYYMMDD, leave 0 for no date">
+                <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 database to download by amplicons, put an amplicons list separated by "," ' help='example: "COI,ITS,16S" or "23S"'/>
-                <param name="bases" type="text" label='Select database to download by base, put a bases list separated by "," ' help='example: "SILVA,PR2,MIDAS" or "BOLD"'/>
-                <param name="filters" type="text" label='Select database to download by filters, put a filters list separated by "," ' help='example: "Pintail100,Fungi"'/>
+                <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 each database"/>
+        <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>
+       	.. image:: static/images/FROGS_logo.png
+   			:height: 144
+   			:width: 110
+
         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.</help>
+        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>