Mercurial > repos > jjohnson > snpsift
annotate snpSift_annotate.xml @ 9:88f4997ccb02 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
| author | jjohnson |
|---|---|
| date | Mon, 11 Apr 2016 09:31:49 -0400 |
| parents | 2f40467536cf |
| children |
| rev | line source |
|---|---|
| 4 | 1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.0"> |
| 0 | 2 <description>SNPs from dbSnp</description> |
| 3 <!-- | |
| 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
| 5 --> | |
| 4 | 6 <macros> |
| 7 <import>snpSift_macros.xml</import> | |
| 8 </macros> | |
| 0 | 9 <expand macro="requirements" /> |
| 4 | 10 <expand macro="stdio" /> |
| 11 <expand macro="version_command" /> | |
| 12 <command><![CDATA[ | |
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2f40467536cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
jjohnson
parents:
6
diff
changeset
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13 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" $annotate_cmd |
| 0 | 14 #if $annotate.id : |
| 15 -id | |
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2f40467536cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
jjohnson
parents:
6
diff
changeset
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16 #elif str($annotate.info_ids).strip() != '' : |
| 0 | 17 -info "$annotate.info_ids" |
| 18 #end if | |
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2f40467536cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
jjohnson
parents:
6
diff
changeset
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19 -q "$dbSnp" "$input" > "$output" |
| 4 | 20 ]]> |
| 0 | 21 </command> |
| 22 <inputs> | |
| 23 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> | |
| 24 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" | |
| 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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824f78c0d0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 915e0f28e6bc2701ca8f333d7b30cf399cd6e9da-dirty
jjohnson
parents:
4
diff
changeset
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30 <param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs" |
| 0 | 31 help="list is a comma separated list of fields. When blank, all INFO fields are included"> |
| 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> | |
| 36 <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> | |
| 37 <help> | |
| 38 This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files). | |
| 39 Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). | |
| 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> | |
| 4 | 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 | |
| 4 | 97 ]]> |
| 0 | 98 </help> |
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2f40467536cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
jjohnson
parents:
6
diff
changeset
|
99 <expand macro="citations" /> |
| 0 | 100 </tool> |
| 101 |