Mercurial > repos > iuc > snpsift
annotate snpSift_annotate.xml @ 13:ed810da439cc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
| author | iuc |
|---|---|
| date | Tue, 07 Jun 2016 09:41:13 -0400 |
| parents | 6bf58286d795 |
| children | 80da7fae14b8 |
| rev | line source |
|---|---|
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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changeset
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1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.0"> |
| 0 | 2 <description>SNPs from dbSnp</description> |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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12
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changeset
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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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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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changeset
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10 <expand macro="stdio" /> |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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11 <expand macro="version_command" /> |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
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changeset
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12 <command><![CDATA[ |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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changeset
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13 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" $annotate_cmd |
| 0 | 14 #if $annotate.id : |
| 15 -id | |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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12
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changeset
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16 #elif str($annotate.info_ids).strip() != '' : |
| 0 | 17 -info "$annotate.info_ids" |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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18 #end if |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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19 -q "$dbSnp" "$input" > "$output" |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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20 ]]> |
| 0 | 21 </command> |
| 22 <inputs> | |
| 23 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> | |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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24 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" |
| 0 | 25 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> |
| 26 <conditional name="annotate"> | |
| 27 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> | |
| 28 <when value="id"/> | |
| 29 <when value="info"> | |
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6bf58286d795
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents:
11
diff
changeset
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30 <param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs" |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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31 help="list is a comma separated list of fields. When blank, all INFO fields are included"> |
| 0 | 32 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> |
| 33 </param> | |
| 34 </when> | |
| 35 </conditional> | |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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36 <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> |
| 0 | 37 <help> |
| 38 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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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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39 Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). |
| 0 | 40 </help> |
| 41 </param> | |
| 42 </inputs> | |
| 43 <outputs> | |
| 44 <data format="vcf" name="output" /> | |
| 45 </outputs> | |
| 46 <tests> | |
| 47 <test> | |
| 48 <param name="input" ftype="vcf" value="annotate_1.vcf"/> | |
| 49 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/> | |
| 50 <param name="annotate_cmd" value="False"/> | |
| 51 <param name="id" value="True"/> | |
| 52 <output name="output"> | |
| 53 <assert_contents> | |
| 54 <has_text text="rs76166080" /> | |
| 55 </assert_contents> | |
| 56 </output> | |
| 57 </test> | |
| 58 </tests> | |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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59 <help><![CDATA[ |
| 0 | 60 |
| 61 This is typically used to annotate IDs from dbSnp. | |
| 62 | |
| 63 Annotatating only the ID field from dbSnp137.vcf :: | |
| 64 | |
| 65 Input VCF: | |
| 66 CHROM POS ID REF ALT QUAL FILTER INFO | |
| 67 22 16157571 . T G 0.0 FAIL NS=53 | |
| 68 22 16346045 . T C 0.0 FAIL NS=244 | |
| 69 22 16350245 . C A 0.0 FAIL NS=192 | |
| 70 | |
| 71 Annotated Output VCF: | |
| 72 #CHROM POS ID REF ALT QUAL FILTER INFO | |
| 73 22 16157571 . T G 0.0 FAIL NS=53 | |
| 74 22 16346045 rs56234788 T C 0.0 FAIL NS=244 | |
| 75 22 16350245 rs2905295 C A 0.0 FAIL NS=192 | |
| 76 | |
| 77 | |
| 78 | |
| 79 Annotatating both the ID and INFO fields from dbSnp137.vcf :: | |
| 80 | |
| 81 Input VCF: | |
| 82 #CHROM POS ID REF ALT QUAL FILTER INFO | |
| 83 22 16157571 . T G 0.0 FAIL NS=53 | |
| 84 22 16346045 . T C 0.0 FAIL NS=244 | |
| 85 22 16350245 . C A 0.0 FAIL NS=192 | |
| 86 | |
| 87 Annotated Output VCF: | |
| 88 #CHROM POS ID REF ALT QUAL FILTER INFO | |
| 89 22 16157571 . T G 0.0 FAIL NS=53 | |
| 90 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 | |
| 91 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 | |
| 92 | |
| 93 | |
| 94 @EXTERNAL_DOCUMENTATION@ | |
| 95 http://snpeff.sourceforge.net/SnpSift.html#annotate | |
| 96 | |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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97 ]]> |
| 0 | 98 </help> |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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99 <expand macro="citations" /> |
| 0 | 100 </tool> |
| 101 |