Mercurial > repos > iuc > snpsift

comparison snpSift_annotate.xml @ 8:5fab4f81391d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit df8a21df77acffe40c0bc0fe0409ca1b529cd7fc"
author iuc
date Sat, 11 Sep 2021 07:17:51 +0000
parents 2b3e65a4252f
children
comparison
equal deleted inserted replaced
7:2e497a770bca 8:5fab4f81391d
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 ln -s '$dbSnp' 'dbSnp.vcf' &&
13 SnpSift -Xmx8G annotate 14 SnpSift -Xmx8G annotate
14 ${annotate.no_info} 15 ${annotate.no_info}
15 #if str($annotate.info_ids).strip(): 16 #if str($annotate.info_ids).strip():
16 -info '$annotate.info_ids' 17 -info '$annotate.info_ids'
17 #end if 18 #end if
18 -q '$dbSnp' '$input' > '$output' 19 -q 'dbSnp.vcf' '$input' > '$output'
19 ]]></command> 20 ]]></command>
20 <inputs> 21 <inputs>
21 <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"/>
22 <param name="dbSnp" type="data" format="vcf" label="VCF File with ID field annotated (e.g. dbSNP.vcf)" 23 <param name="dbSnp" type="data" format="vcf" label="VCF File with ID field annotated (e.g. dbSNP.vcf)"
23 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."/>