diff snpEff.xml @ 16:3790e16a0be0

Add datatype: snpeffdbv4

--- a/snpEff.xml	Tue Oct 21 14:40:44 2014 -0500
+++ b/snpEff.xml	Thu Oct 23 05:09:26 2014 -0500
@@ -34,13 +34,13 @@
         #if $statsFile:
           -stats $statsFile 
         #end if
-        #if $offset.__str__ != '':
+        #if $offset.__str__ != 'default':
           ${offset} 
         #end if
         #if $chr.__str__.strip() != '':
           -chr "$chr" 
         #end if
-        $noLog 
+          $noLog 
         #if $snpDb.genomeSrc == 'cached':
           -dataDir ${snpDb.genomeVersion.fields.path}
           #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
@@ -114,7 +114,7 @@
                 </param>
             </when>
             <when value="history">
-                <param format="snpeffdb" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/>
+                <param format="snpeffdbv4" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/>
                 <!-- From metadata -->
                 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations">
                     <help>These are available for only a few genomes</help>
@@ -130,7 +130,10 @@
                 </param>
             </when>
             <when value="named">
-                <param name="genome_version" type="text" value="GRCh38.76" label="Snpff Version Name"/>
+                <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
+                    <help>http://sourceforge.net/projects/snpeff/files/databases/v4_0/</help>
+                    <validator type="regex" message="A genome version name is required">\S+</validator>
+                </param>
             </when>
         </conditional>
 
@@ -194,7 +197,7 @@
         </param>
 
         <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
-            <option value="" selected="true">Use default (based on input type)</option>
+            <option value="default" selected="true">Use default (based on input type)</option>
             <option value="-0">Force zero-based positions (both input and output)</option>
             <option value="-1">Force one-based positions (both input and output)</option>
         </param>