# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1348261225 18000
# Node ID ef4598ea7179bd4f4a4529263ea47ee01423412b
# Parent  d57983929080fbe98d94e4ed558644bd8d793d71
Add SnpSift dependency

diff -r d57983929080 -r ef4598ea7179 snpEff.xml
--- a/snpEff.xml	Fri Sep 21 15:16:49 2012 -0500
+++ b/snpEff.xml	Fri Sep 21 16:00:25 2012 -0500
@@ -9,7 +9,7 @@
 		<requirement type="package" version="3.0">snpEff</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
-	<command>java -Xmx6G -jar $JAVA_JAR_PATH/snpEff.jar eff -c $JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
+	<command>java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
 	<inputs>
 		<param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
 
diff -r d57983929080 -r ef4598ea7179 snpEff_download.xml
--- a/snpEff_download.xml	Fri Sep 21 15:16:49 2012 -0500
+++ b/snpEff_download.xml	Fri Sep 21 16:00:25 2012 -0500
@@ -4,7 +4,7 @@
 		<requirement type="package" version="3.0">snpEff</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
-	<command>java -jar $JAVA_JAR_PATH/snpEff.jar download -c $JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
+	<command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
 	<inputs>
 		<param name="genomeVersion" type="select" label="Genome">
 				<option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option>
diff -r d57983929080 -r ef4598ea7179 snpSift_annotate.xml
--- a/snpSift_annotate.xml	Fri Sep 21 15:16:49 2012 -0500
+++ b/snpSift_annotate.xml	Fri Sep 21 16:00:25 2012 -0500
@@ -5,10 +5,10 @@
 		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="3.0">snpEff</requirement>
+		<requirement type="package" version="1.7">SnpSift</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
-	<command>java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command>
+	<command>java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -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."/>
diff -r d57983929080 -r ef4598ea7179 snpSift_caseControl.xml
--- a/snpSift_caseControl.xml	Fri Sep 21 15:16:49 2012 -0500
+++ b/snpSift_caseControl.xml	Fri Sep 21 16:00:25 2012 -0500
@@ -5,11 +5,11 @@
 		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="3.0">snpEff</requirement>
+		<requirement type="package" version="1.7">SnpSift</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>
-		java -Xmx1G -jar $JAVA_JAR_PATH/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output
+		java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output
 	</command>
 	<inputs>
 		<param format="vcf" name="input" type="data" label="VCF input"/>
diff -r d57983929080 -r ef4598ea7179 snpSift_filter.xml
--- a/snpSift_filter.xml	Fri Sep 21 15:16:49 2012 -0500
+++ b/snpSift_filter.xml	Fri Sep 21 16:00:25 2012 -0500
@@ -7,11 +7,11 @@
 	java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
 	-->
 	<requirements>
-		<requirement type="package" version="3.0">snpEff</requirement>
+		<requirement type="package" version="1.7">SnpSift</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>
-		java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
+		java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
 	</command>
 	<inputs>
 		<param format="vcf" name="input" type="data" label="VCF input"/>
diff -r d57983929080 -r ef4598ea7179 snpSift_int.xml
--- a/snpSift_int.xml	Fri Sep 21 15:16:49 2012 -0500
+++ b/snpSift_int.xml	Fri Sep 21 16:00:25 2012 -0500
@@ -5,11 +5,11 @@
 		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="3.0">snpEff</requirement>
+		<requirement type="package" version="1.7">SnpSift</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>
-		cat $input | java -Xmx2G -jar $JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output
+		cat $input | java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output
 	</command>
 	<inputs>
 		<param format="vcf" name="input" type="data" label="VCF input"/>
diff -r d57983929080 -r ef4598ea7179 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Sep 21 15:16:49 2012 -0500
+++ b/tool_dependencies.xml	Fri Sep 21 16:00:25 2012 -0500
@@ -20,6 +20,15 @@
         <readme>
         </readme>
     </package>
+    <package name="SnpSift" version="1.7">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">mkdir -p SnpSift; cd SnpSift; wget http://sourceforge.net/projects/snpeff/files/SnpSift_v1_7.jar</action>
+                <action type="set_environment">
+                    <environment_variable name="JAVA_JAR_PATH" action="prepend_to">$INSTALL_DIR/SnpSift</environment_variable>
+                </action>
+            </actions>
+        </install>
 
 </tool_dependency>