Mercurial > repos > iuc > snpsift

annotate snpSift_rmInfo.xml @ 6:2b3e65a4252f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 693e1a3641c776965f68d688c8e1409adba7da1e
author iuc
date Wed, 16 Jan 2019 15:35:26 -0500
parents 09d6806c609e
children
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09d6806c609e 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_rmInfo" name="SnpSift rmInfo" version="@WRAPPER_VERSION@.galaxy0">
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2 <description>remove INFO field annotations</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" />
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[
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10 SnpSift -Xmx2G rmInfo
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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11 '$input'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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12 #echo ' '.join($info_fields.split(','))
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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13 > '$output'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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14 ]]></command>
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15 <inputs>
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16 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
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17 <param name="info_fields" type="text" value="" label="Info fields to remove, e.g. EFF">
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18 <help>Separate multiple INFO fields with a comma, e.g.: EFF,DP</help>
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19 <validator type="empty_field" />
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20 </param>
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21 </inputs>
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22 <outputs>
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23 <data name="output" format="vcf" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input" ftype="vcf" value="test_rmInfo.vcf"/>
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28 <param name="info_fields" value="EFF"/>
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29 <output name="output">
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30 <assert_contents>
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31 <has_text text="DP=29" />
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32 <not_has_text text="EFF=EXON" />
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33 </assert_contents>
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34 </output>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 This command removes INFO fields from a VCF file (i.e. removes annotations)
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39
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40 Removing INFO fields is usually done because you want to re-annotate the VCF file, thus removing old INFO fields in order to add new ones later.
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41
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20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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42 SnpEff & SnpSift only add annotations and do not change current ones. So, in order to re-annotate a file, you should first remove the old annotations and then re-annotate.
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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43 The reason for this behavior is simply because replacing annotation values is considered a bad practice. Imagine that you have a VCF entry in your re-annotated file having the value "AA=1": How do you know if this is from the old annotations or from the new ones? This confusion often leads to problems in downstream steps of your pipelines, so it's better to avoid the problem by first removing all the previous annotations and then adding the new ones.
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45 @EXTERNAL_DOCUMENTATION@
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46 - http://snpeff.sourceforge.net/SnpSift.html#rmInfo
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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47 ]]></help>
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48 <expand macro="citations" />
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49 </tool>