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comparison snpSift_annotate.xml @ 8:2f40467536cf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
author jjohnson
date Sat, 09 Apr 2016 11:53:30 -0400
parents 824f78c0d0df
children
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7:c29f29a6f26c 8:2f40467536cf
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 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd 13 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" $annotate_cmd
14 #if $annotate.id : 14 #if $annotate.id :
15 -id 15 -id
16 #elif $annotate.info_ids.__str__.strip() != '' : 16 #elif str($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 ]]> 20 ]]>
21 </command> 21 </command>
22 <inputs> 22 <inputs>
23 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 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)" 24 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)"
92 92
93 93
94 @EXTERNAL_DOCUMENTATION@ 94 @EXTERNAL_DOCUMENTATION@
95 http://snpeff.sourceforge.net/SnpSift.html#annotate 95 http://snpeff.sourceforge.net/SnpSift.html#annotate
96 96
97 @CITATION_SECTION@
98
99
100 ]]> 97 ]]>
101 </help> 98 </help>
99 <expand macro="citations" />
102 </tool> 100 </tool>
103 101