diff snpSift_filter.xml @ 8:13b6ad2ddace

SnpEffect v3.2

--- a/snpSift_filter.xml	Thu Mar 28 12:29:45 2013 -0500
+++ b/snpSift_filter.xml	Mon May 13 12:45:07 2013 -0500
@@ -1,20 +1,30 @@
-<tool id="snpSift_filter" name="SnpSift Filter" version="3.1">
+<tool id="snpSift_filter" name="SnpSift Filter" version="3.2">
 	<options sanitize="False" />
 	<description>Filter variants using arbitrary expressions</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)
-	java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
-	-->
 	<requirements>
-                <requirement type="package" version="3.1">snpEff</requirement>
+                <requirement type="package" version="3.2">snpEff</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 $inverse $pass 
+                #if $filterId and len($filterId.__str__.strip()) > 0:
+			--filterId = "$filterId"
+                #end if
+                #if $addFilter and len($addFilter.__str__.strip()) > 0:
+			--addFilter = "$addFilter"
+                #end if
+                #if $rmFilter and len($rmFilter.__str__.strip()) > 0:
+			--rmFilter = "$rmFilter"
+                #end if
+ 		> $output
 	</command>
 	<inputs>
 		<param format="vcf" name="input" type="data" label="VCF input"/>
-		<param name="expr" type="text" label="Expression" size="50"/>
+		<param name="expr" type="text" label="Expression" size="120"/>
+		<param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse. Show lines that do not match filter expression"/>
+		<param name="pass" type="boolean" truevalue="--pass" falsevalue="" checked="false" label="Use 'PASS' field instead of filtering out VCF entries"/>
+		<param name="filterId" type="text" value="" optional="true" label="ID for this filter (##FILTER tag in header and FILTER VCF field)." size="10"/>
+		<param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." size="10"/>
+		<param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." size="10"/>
 	</inputs>
 	<configfiles>
 		<configfile name="exprFile">
@@ -37,7 +47,7 @@
                 <param name="expr" value="QUAL >= 50"/>
                 <output name="output">
                     <assert_contents>
-                        <not_has_text text="25967" />
+                        <has_text text="28837706" />
                         <not_has_text text="NT_166464" />
                     </assert_contents>
                 </output>
@@ -56,7 +66,7 @@
 
             <test>
                 <param name="input" ftype="vcf" value="test01.vcf"/>
-                <param name="expr" value="(POS >= 20175 & (POS <= 35549)"/>
+                <param name="expr" value="(POS >= 20175) &amp; (POS &lt;= 35549)"/>
                 <output name="output">
                     <assert_contents>
                         <has_text text="20175" />