Mercurial > repos > iuc > snpsift
annotate snpSift_vcfCheck.xml @ 12:6bf58286d795 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit e5a5ad091c621348dc6ce2df861475ebc54a380e
| author | iuc |
|---|---|
| date | Tue, 13 Oct 2015 17:31:24 -0400 |
| parents | b884686a80dc |
| children | ed810da439cc |
| rev | line source |
|---|---|
| 0 | 1 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="4.0.0"> |
| 2 <description>basic checks for Vcf specification compliance</description> | |
| 3 <macros> | |
| 4 <import>snpSift_macros.xml</import> | |
| 5 </macros> | |
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b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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6 <expand macro="requirements" /> |
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b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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0
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changeset
|
7 <expand macro="stdio" /> |
| 0 | 8 <command> |
| 9 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar vcfCheck $input > $output | |
| 10 </command> | |
| 11 <inputs> | |
| 12 <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data format="vcf" name="output" /> | |
| 16 </outputs> | |
| 17 <tests> | |
| 18 <test> | |
| 19 <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/> | |
| 20 <output name="output"> | |
| 21 <assert_contents> | |
| 22 <has_text text="Errors" /> | |
| 23 </assert_contents> | |
| 24 </output> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help> | |
| 28 | |
| 29 Perform some basic check ups on VCF files to spot common problems. | |
| 30 | |
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11
b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
0
diff
changeset
|
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. |
| 0 | 32 |
| 33 @EXTERNAL_DOCUMENTATION@ | |
| 34 http://snpeff.sourceforge.net/SnpSift.html#vcfCheck | |
| 35 | |
| 36 @CITATION_SECTION@ | |
| 37 | |
| 38 </help> | |
| 39 </tool> |