diff snpEff_databases.xml @ 12:5a29ab10dba6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71

--- a/snpEff_databases.xml	Tue Mar 27 14:56:29 2018 -0400
+++ b/snpEff_databases.xml	Thu Mar 29 20:39:49 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="snpEff_databases" name="SnpEff databases:" version="@wrapper_version@.1">
+<tool id="snpEff_databases" name="SnpEff databases:" version="@wrapper_version@.galaxy1">
     <description> list available databases</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -10,18 +10,18 @@
     <expand macro="version_command" />
     <command><![CDATA[
 
-        snpEff databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/  *//g' 
+        snpEff databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/  *//g'
 
         #if $include_pattern:
-             | grep '${include_pattern}' 
+             | grep '${include_pattern}'
         #end if
 
         #if $exclude_pattern:
-             | grep -v '${exclude_pattern}' 
+             | grep -v '${exclude_pattern}'
         #end if
 
         > '${snpeff_dbs}'
-            
+
     ]]></command>
     <inputs>
         <param name="include_pattern" size="40" type="text" value="" optional="True" label="List entries matching the following expression" help="Databases matching this expression will be listed. Here you can enter text or regular expression. For example, to show only mouse databases use 'Mouse'. Note that this parameter is case-sensitive.">
@@ -69,7 +69,7 @@
     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
 
-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 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).
 
 -------
 
@@ -80,7 +80,7 @@
 There are two ways to use names of databases obtained with this tool in Galaxy's version on snpEff:
 
     #. Use **SnpEff download** tool. It will download the database to the history and you will be able to use it in **SnpEff eff** tool using *Downloaded snpEff database in your history* option of the **Genome source** parameter.
-    #. Use *Download on demand* option of the **SnpEff eff** tool (again, **Genome source** parameter). In this case snpEff will download the database before performing annotation. 
+    #. Use *Download on demand* option of the **SnpEff eff** tool (again, **Genome source** parameter). In this case snpEff will download the database before performing annotation.
 
 @snpeff_in_galaxy_info@
 @external_documentation@