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annotate snpSift_vcfCheck.xml @ 3:20c7d583fec1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
author iuc
date Mon, 12 Jun 2017 10:25:32 -0400
parents bf8c1526871b
children 09d6806c609e
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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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10 SnpSift -Xmx2G vcfCheck
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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11 '$input'
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12 > '$output'
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13 ]]></command>
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14 <inputs>
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15 <param name="input" type="data" format="vcf" label="Variant input file in VCF format to check"/>
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16 </inputs>
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17 <outputs>
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18 <data name="output" format="vcf" />
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19 </outputs>
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20 <tests>
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21 <test expect_exit_code="0">
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22 <param name="input" ftype="vcf" value="test_bad.vcf"/>
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23 <assert_stderr>
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24 <has_text text="Errors" />
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25 </assert_stderr>
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26 </test>
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27 </tests>
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28 <help><![CDATA[
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29 Perform some basic check ups on VCF files to spot common problems.
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30
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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.
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32
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33 @EXTERNAL_DOCUMENTATION@
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34 - http://snpeff.sourceforge.net/SnpSift.html#vcfCheck
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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35 ]]></help>
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36 <expand macro="citations" />
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37 </tool>