Mercurial > repos > iuc > snpsift
comparison snpSift_annotate.xml @ 4:b04635ebfab0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 9d2052269bfbca81a5f9cd10c3153e611358a329
| author | iuc |
|---|---|
| date | Tue, 24 Oct 2017 07:28:17 -0400 |
| parents | 20c7d583fec1 |
| children | 09d6806c609e |
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| 3:20c7d583fec1 | 4:b04635ebfab0 |
|---|---|
| 8 </macros> | 8 </macros> |
| 9 <expand macro="requirements" /> | 9 <expand macro="requirements" /> |
| 10 <expand macro="stdio" /> | 10 <expand macro="stdio" /> |
| 11 <expand macro="version_command" /> | 11 <expand macro="version_command" /> |
| 12 <command><![CDATA[ | 12 <command><![CDATA[ |
| 13 SnpSift annotate | 13 SnpSift -Xmx8G annotate |
| 14 #if $annotate.id == 'id': | 14 #if $annotate.id == 'id': |
| 15 -id | 15 -id |
| 16 #elif str($annotate.info_ids).strip() != '': | 16 #elif str($annotate.info_ids).strip() != '': |
| 17 -info "$annotate.info_ids" | 17 -info "$annotate.info_ids" |
| 18 #end if | 18 #end if |
| 19 -q '$dbSnp' '$input' > '$output' | 19 -q '$dbSnp' '$input' > '$output' |
| 20 ]]></command> | 20 ]]></command> |
| 21 <inputs> | 21 <inputs> |
| 22 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/> | 22 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/> |
| 23 <param name="dbSnp" type="data" format="vcf" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" | 23 <param name="dbSnp" type="data" format="vcf" label="VCF File with ID field annotated (e.g. dbSNP.vcf)" |
| 24 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> | 24 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> |
| 25 <conditional name="annotate"> | 25 <conditional name="annotate"> |
| 26 <param name="id" type="select" label="Fields to annotate"> | 26 <param name="id" type="select" label="Fields to annotate"> |
| 27 <option value="id">Only annotate ID field (no INFO fields will be added)</option> | 27 <option value="id">Only annotate ID field (no INFO fields will be added)</option> |
| 28 <option value="info">Add also INFO fields</option> | 28 <option value="info">Add also INFO fields</option> |