diff data_manager/data_manager_snpEff_download.xml @ 5:8952990fcab9

Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases

--- a/data_manager/data_manager_snpEff_download.xml	Mon Oct 07 10:59:44 2013 -0500
+++ b/data_manager/data_manager_snpEff_download.xml	Wed Nov 27 09:11:32 2013 -0600
@@ -1,7 +1,7 @@
-<tool id="data_manager_snpeff_download" name="SnpEff Download" version="3.3" tool_type="manage_data">
+<tool id="data_manager_snpeff_download" name="SnpEff Download" version="3.4" tool_type="manage_data">
     <description>Download a new database</description>
     <requirements>
-        <requirement type="package" version="3.3">snpEff</requirement>
+        <requirement type="package" version="3.4">snpEff</requirement>
     </requirements>
     <command interpreter="python">
         data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config 
@@ -11,7 +11,9 @@
         </command>
     <inputs>
         <param name="genome_databases" type="select" label="Genome Version">
-            <options from_data_table="snpeff_databases"/>
+            <options from_data_table="snpeff_databases">
+                <filter type="sort_by" column="0" />
+            </options>
         </param>
     </inputs>
 
@@ -41,6 +43,9 @@
 
 For details about this tool, please go to http://snpEff.sourceforge.net
 
+Please cite:
+"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
+
     </help>
 </tool>