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annotate snpSift_vcfCheck.xml @ 13:ed810da439cc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
author iuc
date Tue, 07 Jun 2016 09:41:13 -0400
parents b884686a80dc
children 80da7fae14b8
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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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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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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" />
b884686a80dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
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7 <expand macro="stdio" />
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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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8 <expand macro="version_command" />
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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9 <command><![CDATA[
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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10 java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output"
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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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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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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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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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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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>