# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1413812221 18000
# Node ID 6d429d880a7507a218400b2131bbec93a416a303
# Parent  c5288d5a446e853b20a857503bd5d8d181d1c009
Update for snpeff version 4.0

diff -r c5288d5a446e -r 6d429d880a75 lib/galaxy/datatypes/snpeff.pyc
Binary file lib/galaxy/datatypes/snpeff.pyc has changed
diff -r c5288d5a446e -r 6d429d880a75 readme.rst
--- a/readme.rst	Thu Jun 26 08:40:30 2014 -0500
+++ b/readme.rst	Mon Oct 20 08:37:01 2014 -0500
@@ -9,6 +9,10 @@
     "SnpEff Download" snpEff_download.xml
 are taken from: tool-data/snpeffect_genomedb.loc
 
+There are 2 datamanagers to download and install prebuilt SnpEff Genome databases:
+  data_manager_snpeff_databases - generates a list of available SnpEff genome databases into the tool-data/snpeff_databases.loc 
+  data_manager_snpeff_download - downloads a SnpEff genome database selected from: tool-data/snpeff_databases.loc and adds entries to snpeff_genomedb.loc,snpeff_regulationdb.loc,snpeff_annotations.loc 
+
 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]
 
diff -r c5288d5a446e -r 6d429d880a75 snpEff.xml
--- a/snpEff.xml	Thu Jun 26 08:40:30 2014 -0500
+++ b/snpEff.xml	Mon Oct 20 08:37:01 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="snpEff" name="SnpEff" version="3.6">
+<tool id="snpEff" name="SnpEff" version="4.0.0">
     <description>Variant effect and annotation</description>
     <expand macro="requirements" />
     <macros>
@@ -40,7 +40,7 @@
         #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__ != '':
@@ -176,11 +176,12 @@
             <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline)</option>
             <option value="-canon">Only use canonical transcripts</option>
             <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
-            <option value="-hgvs">Use HGVS annotations for amino acid sub-field</option>
             <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option>
             <option value="-oicr">Add OICR tag in VCF file</option>
             <option value="-onlyReg">Only use regulation tracks</option>
-            <option value="-sequenceOntolgy">Use Sequence Ontolgy terms.</option>
+            <option value="-classic">Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)</option>
+            <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
+            <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
         </param>
         <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
         <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file." help="Format is one transcript ID per line."/>
diff -r c5288d5a446e -r 6d429d880a75 snpEff_download.xml
--- a/snpEff_download.xml	Thu Jun 26 08:40:30 2014 -0500
+++ b/snpEff_download.xml	Mon Oct 20 08:37:01 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="snpEff_download" name="SnpEff Download" version="3.6">
+<tool id="snpEff_download" name="SnpEff Download" version="4.0.0">
     <description>Download a new database</description>
     <expand macro="requirements" />
     <macros>
diff -r c5288d5a446e -r 6d429d880a75 snpEff_macros.xml
--- a/snpEff_macros.xml	Thu Jun 26 08:40:30 2014 -0500
+++ b/snpEff_macros.xml	Mon Oct 20 08:37:01 2014 -0500
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.6">snpEff</requirement>
+            <requirement type="package" version="4.0">snpEff</requirement>
         </requirements>
     </xml>
   <xml name="stdio">
diff -r c5288d5a446e -r 6d429d880a75 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 26 08:40:30 2014 -0500
+++ b/tool_dependencies.xml	Mon Oct 20 08:37:01 2014 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="snpEff" version="3.6">
-        <repository name="package_snpeff_3_6" owner="jjohnson" changeset_revision="849895b37940" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    <package name="snpEff" version="4.0">
+        <repository name="package_snpeff_4_0" owner="jjohnson" changeset_revision="4ac635fc1781" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
 </tool_dependency>