Mercurial > repos > jjohnson > snpeff
diff snpSift_annotate.xml @ 7:0ad9733e22a4
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 29 Nov 2013 09:27:22 -0500 |
| parents | 8952990fcab9 |
| children |
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--- a/snpSift_annotate.xml Thu Nov 28 08:16:11 2013 -0600 +++ b/snpSift_annotate.xml Fri Nov 29 09:27:22 2013 -0500 @@ -1,13 +1,13 @@ <tool id="snpSift_annotate" name="SnpSift Annotate" version="3.4"> - <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="3.4">snpEff</requirement> - </requirements> - <command> + <description>SNPs from dbSnp</description> + <!-- + You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + --> + <expand macro="requirements" /> + <macros> + <import>snpEff_macros.xml</import> + </macros> + <command> java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd #if $annotate.id : -id @@ -15,55 +15,49 @@ -info "$annotate.info_ids" #end if -q $dbSnp $input > $output - </command> - <inputs> - <param format="vcf" name="input" type="data" label="VCF input"/> - <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" - help="The ID field for a variant in input will be assigned from a matching variant in this file."/> - <conditional name="annotate"> - <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> - <when value="id"/> - <when value="info"> - <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs" - help="list is a comma separated list of fields. When blank, all INFO fields are included"> - <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> - </param> - </when> - </conditional> - <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). - Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). - </help> + </command> + <inputs> + <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> + <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."/> + <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="" size="60" 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> - </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> + </when> + </conditional> + <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> + <help> + This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files). + Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). + </help> + </param> + </inputs> + <expand macro="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 - Annotatating only the ID field from dbSnp137.vcf :: Input VCF: @@ -95,13 +89,11 @@ 22 16350245 rs2905295 C A 0.0 FAIL NS=192;RSPOS=16350245;GMAF=0.230804387568556;dbSNPBuildID=101;SSR=1;SAO=0;VP=050000000000000100000140;WGT=0;VC=SNV;GNO -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] +@EXTERNAL_DOCUMENTATION@ -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. +@CITATION_SECTION@ - </help> + </help> </tool>