Mercurial > repos > jjohnson > snpeff
diff snpSift_filter.xml @ 8:13b6ad2ddace
SnpEffect v3.2
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Mon, 13 May 2013 12:45:07 -0500 |
parents | 192a236898f5 |
children | 937367efb1da |
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--- 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) & (POS <= 35549)"/> <output name="output"> <assert_contents> <has_text text="20175" />