Mercurial > repos > iuc > snpsift

annotate snpSift_vcfCheck.xml @ 20:f90f08ed9810 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit df8a21df77acffe40c0bc0fe0409ca1b529cd7fc"
author iuc
date Sat, 11 Sep 2021 07:17:20 +0000
parents ede8954f5c82
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ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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1 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.galaxy0">
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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
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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
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35 ]]></help>
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36 <expand macro="citations" />
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37 </tool>