Mercurial > repos > iuc > snpsift
annotate snpSift_annotate.xml @ 11:b884686a80dc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
| author | iuc |
|---|---|
| date | Mon, 04 May 2015 22:37:06 -0400 |
| parents | f0faaa4d6ee5 |
| children | 6bf58286d795 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="4.0.0"> |
| 2 <description>SNPs from dbSnp</description> | |
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b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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3 <!-- |
| 0 | 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) |
| 5 --> | |
| 6 <macros> | |
| 7 <import>snpSift_macros.xml</import> | |
| 8 </macros> | |
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11
b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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changeset
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9 <expand macro="requirements" /> |
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b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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0
diff
changeset
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10 <expand macro="stdio" /> |
| 0 | 11 <command> |
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11
b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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0
diff
changeset
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12 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd |
| 0 | 13 #if $annotate.id : |
| 14 -id | |
| 15 #elif $annotate.info_ids.__str__.strip() != '' : | |
| 16 -info "$annotate.info_ids" | |
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11
b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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changeset
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17 #end if |
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b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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changeset
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18 -q $dbSnp $input > $output |
| 0 | 19 </command> |
| 20 <inputs> | |
| 21 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> | |
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11
b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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changeset
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22 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" |
| 0 | 23 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> |
| 24 <conditional name="annotate"> | |
| 25 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> | |
| 26 <when value="id"/> | |
| 27 <when value="info"> | |
| 28 <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs" | |
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11
b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
0
diff
changeset
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29 help="list is a comma separated list of fields. When blank, all INFO fields are included"> |
| 0 | 30 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> |
| 31 </param> | |
| 32 </when> | |
| 33 </conditional> | |
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11
b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
0
diff
changeset
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34 <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> |
| 0 | 35 <help> |
| 36 This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files). | |
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11
b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
0
diff
changeset
|
37 Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). |
| 0 | 38 </help> |
| 39 </param> | |
| 40 </inputs> | |
| 41 <outputs> | |
| 42 <data format="vcf" name="output" /> | |
| 43 </outputs> | |
| 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"/> | |
| 48 <param name="annotate_cmd" value="False"/> | |
| 49 <param name="id" value="True"/> | |
| 50 <output name="output"> | |
| 51 <assert_contents> | |
| 52 <has_text text="rs76166080" /> | |
| 53 </assert_contents> | |
| 54 </output> | |
| 55 </test> | |
| 56 </tests> | |
| 57 <help> | |
| 58 | |
| 59 This is typically used to annotate IDs from dbSnp. | |
| 60 | |
| 61 Annotatating only the ID field from dbSnp137.vcf :: | |
| 62 | |
| 63 Input VCF: | |
| 64 CHROM POS ID REF ALT QUAL FILTER INFO | |
| 65 22 16157571 . T G 0.0 FAIL NS=53 | |
| 66 22 16346045 . T C 0.0 FAIL NS=244 | |
| 67 22 16350245 . C A 0.0 FAIL NS=192 | |
| 68 | |
| 69 Annotated Output VCF: | |
| 70 #CHROM POS ID REF ALT QUAL FILTER INFO | |
| 71 22 16157571 . T G 0.0 FAIL NS=53 | |
| 72 22 16346045 rs56234788 T C 0.0 FAIL NS=244 | |
| 73 22 16350245 rs2905295 C A 0.0 FAIL NS=192 | |
| 74 | |
| 75 | |
| 76 | |
| 77 Annotatating both the ID and INFO fields from dbSnp137.vcf :: | |
| 78 | |
| 79 Input VCF: | |
| 80 #CHROM POS ID REF ALT QUAL FILTER INFO | |
| 81 22 16157571 . T G 0.0 FAIL NS=53 | |
| 82 22 16346045 . T C 0.0 FAIL NS=244 | |
| 83 22 16350245 . C A 0.0 FAIL NS=192 | |
| 84 | |
| 85 Annotated Output VCF: | |
| 86 #CHROM POS ID REF ALT QUAL FILTER INFO | |
| 87 22 16157571 . T G 0.0 FAIL NS=53 | |
| 88 22 16346045 rs56234788 T C 0.0 FAIL NS=244;RSPOS=16346045;GMAF=0.162248628884826;dbSNPBuildID=129;SSR=0;SAO=0;VP=050100000000000100000100;WGT=0;VC=SNV;SLO;GNO | |
| 89 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 | |
| 90 | |
| 91 | |
| 92 @EXTERNAL_DOCUMENTATION@ | |
| 93 http://snpeff.sourceforge.net/SnpSift.html#annotate | |
| 94 | |
| 95 @CITATION_SECTION@ | |
| 96 | |
| 97 | |
| 98 </help> | |
| 99 </tool> | |
| 100 |