diff tools/annovar/annovar.xml @ 3:ff5325029a8e draft

Uploaded

--- a/tools/annovar/annovar.xml	Mon Nov 18 10:32:33 2013 -0500
+++ b/tools/annovar/annovar.xml	Thu Apr 10 09:15:32 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="Annovar" name="ANNOVAR" version="2013aug">
+<tool id="AnnovarShed" name="ANNOVAR" version="2013aug">
 	<description> Annotate a file using ANNOVAR </description>
 	
 	<requirements>		
@@ -13,7 +13,8 @@
 		--cosmic63 ${cosmic63}	
 		--cosmic64 ${cosmic64}		
 		--cosmic65 ${cosmic65}
-		--cosmic67 ${cosmic67}			
+		--cosmic67 ${cosmic67}
+		--cosmic68 ${cosmic68}
 		--outall ${annotated}		
 		--outinvalid ${invalid}
 		--dorunannovar ${dorun}
@@ -130,7 +131,9 @@
 			<option value="snp135"          > 135            (hg19 only) </option>	
 			<option value="snp135NonFlagged"> 135 NonFlagged  </option>
 			<option value="snp137"          > 137            (hg19 only) </option>				
-			<option value="snp137NonFlagged"> 137 NonFlagged  </option>			
+			<option value="snp137NonFlagged"> 137 NonFlagged  </option>
+			<option value="snp138"          > 138            (hg19 only) </option>				
+			<option value="snp138NonFlagged"> 138 NonFlagged  </option>				
 		</param>	
 
 		<param name="ver1000g" type="select" label="Select 1000Genomes Annotation(s)" multiple="true" display="checkboxes"  optional="true" help="2012april database for ALL populations was converted to hg18 using the UCSC liftover program">			
@@ -159,7 +162,7 @@
 
 		<param name="gerp" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="GERP++ Annotation?" help="GERP identifies constrained elements in multiple alignments by quantifying substitution deficits (see http://mendel.stanford.edu/SidowLab/downloads/gerp/ for details) This option annotates those variants having GERP++>2 in human genome, as this threshold is typically regarded as evolutionarily conserved and potentially functional"/>
 	
-		<param name="clinvar" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="CLINVAR Annotation? (hg19 only)" help="version 2013-11-05. Annotations include Variant Clinical Significance (unknown, untested, non-pathogenic, probable-non-pathogenic, probable-pathogenic, pathogenic, drug-response, histocompatibility, other) and Variant disease name."/>
+		<param name="clinvar" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="CLINVAR Annotation? (hg19 only)" help="version 2014-02-11. Annotations include Variant Clinical Significance (unknown, untested, non-pathogenic, probable-non-pathogenic, probable-pathogenic, pathogenic, drug-response, histocompatibility, other) and Variant disease name."/>
 		<param name="nci60" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with NCI60? (hg19 only)" help="NCI-60 exome allele frequency data"/>
 		<param name="cgfortysix" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Complete Genomics 46 Genomes?" help="Diversity Panel; 46 unrelated individuals"/>
 		<param name="cgsixtynine" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Complete Genomics 69 Genomes?" help="Diversity Panel, Pedigree, YRI trio and PUR trio"/>
@@ -168,6 +171,8 @@
 		<param name="cosmic64" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC64? (hg19 only)"/>
 		<param name="cosmic65" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC65? (hg19 only)"/>
 		<param name="cosmic67" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC67? (hg19 only)"/>
+		<param name="cosmic68" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC68? (hg19 only)"/>
+
 		
 		<param name="newimpactscores" type="select" label="Select functional impact scores (LJB2)" multiple="true" display="checkboxes" optional="true" help="LJB refers to Liu, Jian, Boerwinkle paper in Human Mutation, pubmed ID 21520341. ">						
 			<option value="ljb2_sift"> SIFT score </option>