Mercurial > repos > jjohnson > snpeff
diff snpSift_filter.xml @ 5:8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 27 Nov 2013 09:11:32 -0600 |
| parents | 6ad9205c1307 |
| children | 0ad9733e22a4 |
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--- a/snpSift_filter.xml Mon Oct 07 10:59:44 2013 -0500 +++ b/snpSift_filter.xml Wed Nov 27 09:11:32 2013 -0600 @@ -1,98 +1,123 @@ -<tool id="snpSift_filter" name="SnpSift Filter" version="3.3"> - <options sanitize="False" /> - <description>Filter variants using arbitrary expressions</description> - <requirements> - <requirement type="package" version="3.3">snpEff</requirement> - </requirements> - <command> - java -Xmx6G -jar \$SNPEFF_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" +<tool id="snpSift_filter" name="SnpSift Filter" version="3.4"> + <options sanitize="False" /> + <description>Filter variants using arbitrary expressions</description> + <requirements> + <requirement type="package" version="3.4">snpEff</requirement> + </requirements> + <command> + java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse + #if $filtering.mode == 'field': + #if $filtering.replace.pass: + --pass + #if $filtering.replace.filterId and len($filtering.replace.filterId.__str__.strip()) > 0: + --filterId "$filtering.replace.filterId" #end if - > $output - </command> - <inputs> - <param format="vcf" name="input" type="data" label="VCF input"/> - <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"> - $expr - </configfile> - </configfiles> - - <outputs> - <data format="vcf" name="output" /> - </outputs> - <stdio> - <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> - - <tests> + #end if + #if $filtering.addFilter and len($filtering.addFilter.__str__.strip()) > 0: + --addFilter "$filtering.addFilter" + #end if + #if $filtering.rmFilter and len($filtering.rmFilter.__str__.strip()) > 0: + --rmFilter "$filtering.rmFilter" + #end if + #end if + > $output + </command> + <inputs> + <param format="vcf" name="input" type="data" label="VCF input"/> + <param name="expr" type="text" label="Expression" size="160"/> + <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse. Show lines that do not match filter expression"/> + <conditional name="filtering"> + <param name="mode" type="select" labael="Filter mode"> + <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option> + <option value="field">Change the FILTER field, but retain all entries</option> + </param> + <when value="entries"/> + <when value="field"> + <conditional name="replace"> + <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'" + help="appends an ID tag to non-matching entry FILTER "/> + <when value="no"/> + <when value="yes"> + <param name="filterId" type="text" value="" optional="true" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)." size="10" + help="Default ID is 'SnpSift'"/> + </when> + </conditional> + <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"/> + </when> + </conditional> + </inputs> + <configfiles> + <configfile name="exprFile"> + $expr + </configfile> + </configfiles> - <test> - <param name="input" ftype="vcf" value="test01.vcf"/> - <param name="expr" value="QUAL >= 50"/> - <output name="output"> - <assert_contents> - <has_text text="28837706" /> - <not_has_text text="NT_166464" /> - </assert_contents> - </output> - </test> + <outputs> + <data format="vcf" name="output" /> + </outputs> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + + <tests> - <test> - <param name="input" ftype="vcf" value="test01.vcf"/> - <param name="expr" value="(CHROM = '19')"/> - <output name="output"> - <assert_contents> - <has_text text="3205820" /> - <not_has_text text="NT_16" /> - </assert_contents> - </output> - </test> + <test> + <param name="input" ftype="vcf" value="test01.vcf"/> + <param name="expr" value="QUAL >= 50"/> + <param name="mode" value="entries"/> + <output name="output"> + <assert_contents> + <has_text text="28837706" /> + <not_has_text text="NT_166464" /> + </assert_contents> + </output> + </test> - <test> - <param name="input" ftype="vcf" value="test01.vcf"/> - <param name="expr" value="(POS >= 20175) & (POS <= 35549)"/> - <output name="output"> - <assert_contents> - <has_text text="20175" /> - <has_text text="35549" /> - <has_text text="22256" /> - <not_has_text text="18933" /> - <not_has_text text="37567" /> - </assert_contents> - </output> - </test> + <test> + <param name="input" ftype="vcf" value="test01.vcf"/> + <param name="expr" value="(CHROM = '19')"/> + <param name="mode" value="entries"/> + <output name="output"> + <assert_contents> + <has_text text="3205820" /> + <not_has_text text="NT_16" /> + </assert_contents> + </output> + </test> - <test> - <param name="input" ftype="vcf" value="test01.vcf"/> - <param name="expr" value="( DP >= 5 )"/> - <output name="output"> - <assert_contents> - <has_text text="DP=5;" /> - <has_text text="DP=6;" /> - <not_has_text text="DP=1;" /> - </assert_contents> - </output> - </test> + <test> + <param name="input" ftype="vcf" value="test01.vcf"/> + <param name="expr" value="(POS >= 20175) & (POS <= 35549)"/> + <param name="mode" value="entries"/> + <output name="output"> + <assert_contents> + <has_text text="20175" /> + <has_text text="35549" /> + <has_text text="22256" /> + <not_has_text text="18933" /> + <not_has_text text="37567" /> + </assert_contents> + </output> + </test> - </tests> + <test> + <param name="input" ftype="vcf" value="test01.vcf"/> + <param name="expr" value="( DP >= 5 )"/> + <param name="mode" value="entries"/> + <output name="output"> + <assert_contents> + <has_text text="DP=5;" /> + <has_text text="DP=6;" /> + <not_has_text text="DP=1;" /> + </assert_contents> + </output> + </test> - <help> + </tests> + + <help> **SnpSift filter** @@ -123,5 +148,12 @@ For complete details about this tool and epressions that can be used, please go to http://snpeff.sourceforge.net/SnpSift.html#filter - </help> +SnpEff citation: +"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] + +SnpSift citation: +"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012. + + + </help> </tool>