Mercurial > repos > jjohnson > snpeff
annotate snpSift_annotate.xml @ 9:937367efb1da default tip
Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 18 Sep 2013 10:49:56 -0500 |
| parents | 13b6ad2ddace |
| children |
| rev | line source |
|---|---|
| 8 | 1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="3.2"> |
| 0 | 2 <description>Annotate SNPs from dbSnp</description> |
| 3 <!-- | |
| 4 You will need to change the path to wherever your installation is. | |
| 5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
| 6 --> | |
| 7 <requirements> | |
| 8 | 8 <requirement type="package" version="3.2">snpEff</requirement> |
| 0 | 9 </requirements> |
| 8 | 10 <command> |
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9
937367efb1da
Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
Jim Johnson <jj@umn.edu>
parents:
8
diff
changeset
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11 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd |
| 8 | 12 #if $annotate.id : |
| 13 -id | |
| 14 #elif $annotate.info_ids.__str__.strip() != '' : | |
| 15 -info "$annotate.info_ids" | |
| 16 #end if | |
| 17 -q $dbSnp $input > $output | |
| 18 </command> | |
| 0 | 19 <inputs> |
| 20 <param format="vcf" name="input" type="data" label="VCF input"/> | |
| 8 | 21 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" |
| 22 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> | |
| 23 <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Annotate in Memory" | |
| 24 help="allows unsorted VCF files, but it loads the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files)"/> | |
| 25 <conditional name="annotate"> | |
| 26 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> | |
| 27 <when value="id"/> | |
| 28 <when value="info"> | |
| 29 <param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs" | |
| 30 help="list is a comma separated list of fields. When blank, all INFO fields are included"> | |
| 31 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> | |
| 32 </param> | |
| 33 </when> | |
| 34 </conditional> | |
| 0 | 35 </inputs> |
| 36 <stdio> | |
| 37 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 38 <exit_code range="1:" level="fatal" description="Error" /> | |
| 39 </stdio> | |
| 40 | |
| 41 <outputs> | |
| 42 <data format="vcf" name="output" /> | |
| 43 </outputs> | |
| 5 | 44 <tests> |
| 45 <test> | |
| 46 <param name="input" ftype="vcf" value="annotate_1.vcf"/> | |
| 47 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/> | |
| 8 | 48 <param name="annotate_cmd" value="False"/> |
| 49 <param name="id" value="True"/> | |
| 5 | 50 <output name="output"> |
| 51 <assert_contents> | |
| 52 <has_text text="rs76166080" /> | |
| 53 </assert_contents> | |
| 54 </output> | |
| 55 </test> | |
| 56 </tests> | |
| 0 | 57 <help> |
| 58 | |
| 59 This is typically used to annotate IDs from dbSnp. | |
| 60 | |
| 61 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate | |
| 62 | |
| 63 </help> | |
| 64 </tool> | |
| 65 |