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comparison snpSift_annotate.xml @ 4:baf6602903e1

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author jjohnson
date Wed, 09 Dec 2015 14:03:26 -0500
parents 796388c291d3
children 824f78c0d0df
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3:1739678def32 4:baf6602903e1
1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="4.0.0"> 1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.0">
2 <description>SNPs from dbSnp</description> 2 <description>SNPs from dbSnp</description>
3 <!-- 3 <!--
4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
5 --> 5 -->
6 <macros>
7 <import>snpSift_macros.xml</import>
8 </macros>
6 <expand macro="requirements" /> 9 <expand macro="requirements" />
7 <macros> 10 <expand macro="stdio" />
8 <import>snpEff_macros.xml</import> 11 <expand macro="version_command" />
9 </macros> 12 <command><![CDATA[
10 <command>
11 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd 13 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd
12 #if $annotate.id : 14 #if $annotate.id :
13 -id 15 -id
14 #elif $annotate.info_ids.__str__.strip() != '' : 16 #elif $annotate.info_ids.__str__.strip() != '' :
15 -info "$annotate.info_ids" 17 -info "$annotate.info_ids"
16 #end if 18 #end if
17 -q $dbSnp $input > $output 19 -q $dbSnp $input > $output
20 ]]>
18 </command> 21 </command>
19 <inputs> 22 <inputs>
20 <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"/>
21 <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)"
22 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> 25 help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
35 This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files). 38 This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files).
36 Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). 39 Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files).
37 </help> 40 </help>
38 </param> 41 </param>
39 </inputs> 42 </inputs>
40 <expand macro="stdio" />
41 <outputs> 43 <outputs>
42 <data format="vcf" name="output" /> 44 <data format="vcf" name="output" />
43 </outputs> 45 </outputs>
44 <tests> 46 <tests>
45 <test> 47 <test>
52 <has_text text="rs76166080" /> 54 <has_text text="rs76166080" />
53 </assert_contents> 55 </assert_contents>
54 </output> 56 </output>
55 </test> 57 </test>
56 </tests> 58 </tests>
57 <help> 59 <help><![CDATA[
58 60
59 This is typically used to annotate IDs from dbSnp. 61 This is typically used to annotate IDs from dbSnp.
60 62
61 Annotatating only the ID field from dbSnp137.vcf :: 63 Annotatating only the ID field from dbSnp137.vcf ::
62 64
93 http://snpeff.sourceforge.net/SnpSift.html#annotate 95 http://snpeff.sourceforge.net/SnpSift.html#annotate
94 96
95 @CITATION_SECTION@ 97 @CITATION_SECTION@
96 98
97 99
100 ]]>
98 </help> 101 </help>
99 </tool> 102 </tool>
100 103