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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
author jjohnson
date Mon, 11 Apr 2016 09:31:49 -0400
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1 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.0">
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2 <description>basic checks for Vcf specification compliance</description>
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3 <macros>
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4 <import>snpSift_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command><![CDATA[
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2f40467536cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
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10 java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output"
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11 ]]>
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12 </command>
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13 <inputs>
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14 <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/>
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15 </inputs>
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16 <outputs>
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17 <data format="vcf" name="output" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/>
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22 <output name="output">
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23 <assert_contents>
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24 <has_text text="Errors" />
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25 </assert_contents>
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26 </output>
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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31 Perform some basic check ups on VCF files to spot common problems.
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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.
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34
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35 @EXTERNAL_DOCUMENTATION@
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36 http://snpeff.sourceforge.net/SnpSift.html#vcfCheck
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38 ]]>
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39 </help>
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40 <expand macro="citations" />
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41 </tool>