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comparison snpSift_rmInfo.xml @ 11:b884686a80dc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:37:06 -0400
parents f0faaa4d6ee5
children ed810da439cc
comparison
equal deleted inserted replaced
10:93577c5e76ec 11:b884686a80dc
1 <tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="4.0.0"> 1 <tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="4.0.0">
2 <description>remove INFO field annotations</description> 2 <description>remove INFO field annotations</description>
3 <expand macro="requirements" />
4 <macros> 3 <macros>
5 <import>snpSift_macros.xml</import> 4 <import>snpSift_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
7 <command> 8 <command>
8 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar rmInfo $input ' '.join($info_fields.split(',')) > $output 9 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar rmInfo $input ' '.join($info_fields.split(',')) > $output
9 </command> 10 </command>
10 <inputs> 11 <inputs>
11 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 12 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
15 </param> 16 </param>
16 </inputs> 17 </inputs>
17 <outputs> 18 <outputs>
18 <data format="vcf" name="output" /> 19 <data format="vcf" name="output" />
19 </outputs> 20 </outputs>
20 <expand macro="stdio" />
21 <tests> 21 <tests>
22 <test> 22 <test>
23 <param name="input" ftype="vcf" value="test-data/test_rmInfo.vcf"/> 23 <param name="input" ftype="vcf" value="test-data/test_rmInfo.vcf"/>
24 <param name="info_fields" value="EFF"/> 24 <param name="info_fields" value="EFF"/>
25 <output name="output"> 25 <output name="output">
40 </test> 40 </test>
41 </tests> 41 </tests>
42 <help> 42 <help>
43 This command removes INFO fields from a VCF file (i.e. removes annotations) 43 This command removes INFO fields from a VCF file (i.e. removes annotations)
44 44
45 Removing INFO fields is usually done because you want to re-annotate the VCF file, thus removing old INFO fields in order to add new ones later. 45 Removing INFO fields is usually done because you want to re-annotate the VCF file, thus removing old INFO fields in order to add new ones later.
46 46
47 SnpEff &amp; SnpSift only add annotations and do not change current ones. So, in order to re-annotate a file, you should first remove the old annotations and then re-annotate. 47 SnpEff &amp; SnpSift only add annotations and do not change current ones. So, in order to re-annotate a file, you should first remove the old annotations and then re-annotate.
48 The reason for this behavior is simply because replacing annotation values is considered a bad practice. Imagine that you have a VCF entry in your re-annotated file having the value "AA=1": How do you know if this is from the old annotations or from the new ones? This confusion often leads to problems in downstream steps of your pipelines, so it's better to avoid the problem by first removing all the previous annotations and then adding the new ones. 48 The reason for this behavior is simply because replacing annotation values is considered a bad practice. Imagine that you have a VCF entry in your re-annotated file having the value "AA=1": How do you know if this is from the old annotations or from the new ones? This confusion often leads to problems in downstream steps of your pipelines, so it's better to avoid the problem by first removing all the previous annotations and then adding the new ones.
49 49
50 @EXTERNAL_DOCUMENTATION@ 50 @EXTERNAL_DOCUMENTATION@
51 http://snpeff.sourceforge.net/SnpSift.html#rmInfo 51 http://snpeff.sourceforge.net/SnpSift.html#rmInfo
52 52
53 @CITATION_SECTION@ 53 @CITATION_SECTION@