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comparison snpSift_vcfCheck.xml @ 4:baf6602903e1

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author jjohnson
date Wed, 09 Dec 2015 14:03:26 -0500
parents 1739678def32
children 2f40467536cf
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3:1739678def32 4:baf6602903e1
1 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="4.0.0"> 1 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.0">
2 <description>basic checks for Vcf specification compliance</description> 2 <description>basic checks for Vcf specification compliance</description>
3 <macros>
4 <import>snpSift_macros.xml</import>
5 </macros>
3 <expand macro="requirements" /> 6 <expand macro="requirements" />
4 <macros> 7 <expand macro="stdio" />
5 <import>snpEff_macros.xml</import> 8 <expand macro="version_command" />
6 </macros> 9 <command><![CDATA[
7 <command>
8 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar vcfCheck $input > $output 10 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar vcfCheck $input > $output
11 ]]>
9 </command> 12 </command>
10 <inputs> 13 <inputs>
11 <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/> 14 <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/>
12 </inputs> 15 </inputs>
13 <outputs> 16 <outputs>
14 <data format="vcf" name="output" /> 17 <data format="vcf" name="output" />
15 </outputs> 18 </outputs>
16 <expand macro="stdio" />
17 <tests> 19 <tests>
18 <test> 20 <test>
19 <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/> 21 <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/>
20 <output name="output"> 22 <output name="output">
21 <assert_contents> 23 <assert_contents>
22 <has_text text="Errors" /> 24 <has_text text="Errors" />
23 </assert_contents> 25 </assert_contents>
24 </output> 26 </output>
25 </test> 27 </test>
26 </tests> 28 </tests>
27 <help> 29 <help><![CDATA[
28 30
29 Perform some basic check ups on VCF files to spot common problems. 31 Perform some basic check ups on VCF files to spot common problems.
30 32
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. 33 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 34
33 @EXTERNAL_DOCUMENTATION@ 35 @EXTERNAL_DOCUMENTATION@
34 http://snpeff.sourceforge.net/SnpSift.html#vcfCheck 36 http://snpeff.sourceforge.net/SnpSift.html#vcfCheck
35 37
36 @CITATION_SECTION@ 38 @CITATION_SECTION@
37 39
40 ]]>
38 </help> 41 </help>
39 </tool> 42 </tool>