--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpSift_annotate.xml	Thu Jul 04 10:43:55 2013 -0400
@@ -0,0 +1,65 @@
+<tool id="snpSift_annotate" name="SnpSift Annotate" version="3.2">
+	<description>Annotate SNPs from dbSnp</description>
+	<!-- 
+	    You will need to change the path to wherever your installation is.
+		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
+	-->
+	<requirements>
+                <requirement type="package" version="3.2">snpEff</requirement>
+	</requirements>
+	<command>
+        java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar $annotate_cmd 
+        #if $annotate.id :
+          -id
+        #elif $annotate.info_ids.__str__.strip() != '' :
+          -info "$annotate.info_ids"
+        #end if          
+        -q $dbSnp $input > $output 
+        </command>
+	<inputs>
+		<param format="vcf" name="input" type="data" label="VCF input"/>
+		<param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" 
+                       help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
+		<param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Annotate in Memory" 
+                       help="allows unsorted VCF files, but it loads the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files)"/>
+                <conditional name="annotate">
+			<param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/>
+			<when value="id"/>
+			<when value="info">
+				<param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs"
+                                       help="list is a comma separated list of fields. When blank, all INFO fields are included">	
+					<validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
+				</param>
+			</when>
+                </conditional>
+	</inputs>
+        <stdio>
+          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+          <exit_code range="1:"  level="fatal"   description="Error" />
+        </stdio>
+
+	<outputs>
+		<data format="vcf" name="output" />
+	</outputs>
+	<tests>
+	    <test>
+                <param name="input" ftype="vcf" value="annotate_1.vcf"/>
+                <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
+                <param name="annotate_cmd" value="False"/>
+                <param name="id" value="True"/>
+                <output name="output">
+                    <assert_contents>
+                        <has_text text="rs76166080" />
+                    </assert_contents>
+                </output>
+	    </test>
+	</tests>
+	<help>
+
+This is typically used to annotate IDs from dbSnp.
+
+For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate
+
+	</help>
+</tool>
+