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annotate snpSift_vcfCheck.xml @ 1:98708b88af9f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
author iuc
date Tue, 07 Jun 2016 10:04:09 -0400
parents 9e8280e19338
children bf8c1526871b
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98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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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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98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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6 <expand macro="requirements" />
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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7 <expand macro="stdio" />
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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8 <expand macro="version_command" />
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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9 <command><![CDATA[
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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10 java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output"
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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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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37
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98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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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>