diff snpEff_databases.xml @ 29:ca2b512e8d7c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7

--- a/snpEff_databases.xml	Sat Sep 28 16:27:56 2024 +0000
+++ b/snpEff_databases.xml	Mon Oct 21 13:56:15 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="snpEff_databases" name="SnpEff databases:" version="@WRAPPER_VERSION@.galaxy2">
+<tool id="snpEff_databases" name="SnpEff databases:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
     <description> list available databases</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -19,6 +19,10 @@
              | grep -v '${exclude_pattern}'
         #end if
 
+        #if str($include_download_path) == "no":
+            | cut -f 1,2,3,4
+        #end if
+
         > '${snpeff_dbs}'
     ]]></command>
     <inputs>
@@ -38,7 +42,10 @@
                 </valid>
             </sanitizer>
         </param>
-
+        <param name="include_download_path" type="select" display="radio" label="Include download paths?" help="When snpEff dumps the list of available databases, it includes their download paths. These are not needed in the Galaxy context.">
+            <option value="yes">Yes</option>
+            <option value="no" selected="true">No</option>
+        </param>
     </inputs>
     <outputs>
         <data name="snpeff_dbs" format="tabular" label="${tool.name} @SNPEFF_VERSION@ available databases" />
@@ -63,12 +70,16 @@
     <help><![CDATA[
 **What it does**
 
-This tool downloads the master list of snpEff databases from @SNPEFF_DATABASE_URL@. You can then look at this list and decide which database to use for your analysis. For example, if **List entries matching the following expression** parameter of this tool is set to *Mouse* the it will produce a tabular dataset with the following content::
+This tool downloads the master list of snpEff databases from a remote SnpEff repository. You can then look at this list and decide which database to use for your analysis. For example, if **List entries matching the following expression** parameter of this tool is set to *Mouse*, it will produce a tabular dataset with the following content::
 
-    mm10  Mouse  http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_mm10.zip
-    mm9   Mouse  http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_mm9.zip
+    mm10  Mouse
+    mm39  Mouse
+    mm9   Mouse
 
-This means that there two available snpEff databases for mouse genome versions mm9 and mm10. In order to download these databases you should use identifier from the first column (e.g., mm9 or mm10 in this case).
+This means that there are three available snpEff databases for mouse genome. If you want to use mm39 in you analysis:
+
+ - set **Genome source** option of **SnpEff eff** Galaxy tool to *Download on demand*
+ - enter 'mm39' into **Snpff Genome Version Name** text box
 
 -------
 
@@ -83,6 +94,7 @@
 
 @SNPEFF_IN_GALAXY_INFO@
 @EXTERNAL_DOCUMENTATION@
+
     ]]></help>
     <expand macro="citations" />
 </tool>