diff snpEff_macros.xml @ 1:500832f27cbc draft

Uploaded

--- a/snpEff_macros.xml	Wed Dec 11 08:53:32 2013 -0500
+++ b/snpEff_macros.xml	Thu Jan 22 08:28:37 2015 -0500
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.4">snpEff</requirement>
+            <requirement type="package" version="4.0">snpEff</requirement>
         </requirements>
     </xml>
   <xml name="stdio">
@@ -10,9 +10,13 @@
         <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
   </xml>
+  <token name="@WRAPPER_VERSION@">4.0</token>
+  <token name="@SNPEFF_VERSION@">SnpEff4.0</token>
+  <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_0/</token>
   <token name="@EXTERNAL_DOCUMENTATION@">
 
-For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals
+For details about this tool, please go to:
+	http://snpeff.sourceforge.net/SnpEff_manual.html
 
   </token>
   <token name="@CITATION_SECTION@">------
@@ -22,10 +26,13 @@
 For the underlying tool, please cite the following two publications:
 
 SnpEff citation:
-"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]
-
-SnpSift citation:
-"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
+"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 6(2):80-92, 2012
 
   </token>
+  <xml name="citations">
+      <citations>
+        <citation type="doi">10.4161/fly.19695</citation>
+        <yield />
+      </citations>
+  </xml>
 </macros>