# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1413812580 18000
# Node ID 796388c291d395e5f78e44f9a013932673f9c309
# Parent  1ae5526db990a937a1625d25bd4c6d7981d53117
Update for snpeff version 4.0

diff -r 1ae5526db990 -r 796388c291d3 snpEff_macros.xml
--- a/snpEff_macros.xml	Thu Jun 26 09:22:13 2014 -0400
+++ b/snpEff_macros.xml	Mon Oct 20 08:43:00 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 1ae5526db990 -r 796388c291d3 snpSift_annotate.xml
--- a/snpSift_annotate.xml	Thu Jun 26 09:22:13 2014 -0400
+++ b/snpSift_annotate.xml	Mon Oct 20 08:43:00 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="snpSift_annotate" name="SnpSift Annotate" version="3.6">
+<tool id="snpSift_annotate" name="SnpSift Annotate" version="4.0.0">
     <description>SNPs from dbSnp</description>
     <!-- 
         You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
diff -r 1ae5526db990 -r 796388c291d3 snpSift_caseControl.xml
--- a/snpSift_caseControl.xml	Thu Jun 26 09:22:13 2014 -0400
+++ b/snpSift_caseControl.xml	Mon Oct 20 08:43:00 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.6">
+<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="4.0.0">
     <description>Count samples are in 'case' and 'control' groups.</description>
     <!-- 
         You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
diff -r 1ae5526db990 -r 796388c291d3 snpSift_filter.xml
--- a/snpSift_filter.xml	Thu Jun 26 09:22:13 2014 -0400
+++ b/snpSift_filter.xml	Mon Oct 20 08:43:00 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="snpSift_filter" name="SnpSift Filter" version="3.6">
+<tool id="snpSift_filter" name="SnpSift Filter" version="4.0.0">
     <options sanitize="False" />
     <description>Filter variants using arbitrary expressions</description>
     <expand macro="requirements" />
@@ -50,7 +50,7 @@
     </inputs>
     <configfiles>
         <configfile name="exprFile">
-        $expr
+$expr#slurp
         </configfile> 
     </configfiles>
 
@@ -119,13 +119,36 @@
 
 Some examples:
 
+  - *I want just the variants from the second million bases of chr1*:
+
+    ::
+
+    ( CHROM = 'chr1' ) &amp; ( POS &gt; 1000000 )  &amp; ( POS &lt; 2000000 )
+
+  - *Filter value is either 'PASS' or it is missing*:
+
+    ::
+
+    (FILTER = 'PASS') | ( na FILTER )  
+
+  - *I want to filter lines with an EFF of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*:
+
+    ::
+  
+    ( EFF[*].EFFECT = 'frameshift_variant' )
+
+  - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*:
+
+    ::
+  
+    ( EFF[*].EFFECT = 'FRAME_SHIFT' )
+
   - *I want to filter out samples with quality less than 30*:
 
     ::
 
     ( QUAL &gt; 30 )
-     
-     
+
   - *...but we also want InDels that have quality 20 or more*:
 
     ::
@@ -151,12 +174,11 @@
     (isHom( GEN[0] ) &amp; isVariant( GEN[0] ) &amp; isRef( GEN[1] ))
 
 
-  - *I want to filter lines with an EFF of FRAME_SHIFT*:
+**For information regarding HGVS and Sequence Ontology terms versus classic names**:
 
-    ::
-  
-    ( EFF[*].EFFECT = 'FRAME_SHIFT' )
-  
+  - http://snpeff.sourceforge.net/SnpEff_manual.html#cmdline for the options: -classic, -hgvs, and -sequenceOntology
+  - http://snpeff.sourceforge.net/SnpEff_manual.html#input for the table containing the classic name and sequence onology term for each effect
+
 
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#filter
diff -r 1ae5526db990 -r 796388c291d3 snpSift_int.xml
--- a/snpSift_int.xml	Thu Jun 26 09:22:13 2014 -0400
+++ b/snpSift_int.xml	Mon Oct 20 08:43:00 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="snpSift_int" name="SnpSift Intervals" version="3.6">
+<tool id="snpSift_int" name="SnpSift Intervals" version="4.0.0">
     <description>Filter variants using intervals</description>
     <!-- 
         You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
diff -r 1ae5526db990 -r 796388c291d3 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 26 09:22:13 2014 -0400
+++ b/tool_dependencies.xml	Mon Oct 20 08:43:00 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>