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comparison snpSift_vcfCheck.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
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10:93577c5e76ec 11:b884686a80dc
1 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="4.0.0"> 1 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="4.0.0">
2 <description>basic checks for Vcf specification compliance</description> 2 <description>basic checks for Vcf specification compliance</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 vcfCheck $input > $output 9 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar vcfCheck $input > $output
9 </command> 10 </command>
10 <inputs> 11 <inputs>
11 <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/> 12 <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/>
12 </inputs> 13 </inputs>
13 <outputs> 14 <outputs>
14 <data format="vcf" name="output" /> 15 <data format="vcf" name="output" />
15 </outputs> 16 </outputs>
16 <expand macro="stdio" />
17 <tests> 17 <tests>
18 <test> 18 <test>
19 <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/> 19 <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/>
20 <output name="output"> 20 <output name="output">
21 <assert_contents> 21 <assert_contents>
26 </tests> 26 </tests>
27 <help> 27 <help>
28 28
29 Perform some basic check ups on VCF files to spot common problems. 29 Perform some basic check ups on VCF files to spot common problems.
30 30
31 SnpSift vcfCheck checks for some common problems where VCF files are not following the specification. Given that many common VCF problems cause analysis tools and pipelines to behave unexpectedly, this command is intended as a simple debugging tool. 31 SnpSift vcfCheck checks for some common problems where VCF files are not following the specification. Given that many common VCF problems cause analysis tools and pipelines to behave unexpectedly, this command is intended as a simple debugging tool.
32 32
33 @EXTERNAL_DOCUMENTATION@ 33 @EXTERNAL_DOCUMENTATION@
34 http://snpeff.sourceforge.net/SnpSift.html#vcfCheck 34 http://snpeff.sourceforge.net/SnpSift.html#vcfCheck
35 35
36 @CITATION_SECTION@ 36 @CITATION_SECTION@