Mercurial > repos > iuc > snpsift

annotate snpSift_rmInfo.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_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" />
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8 <expand macro="version_command" />
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9 <command><![CDATA[
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10 SnpSift -Xmx2G rmInfo
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11 '$input'
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12 #echo ' '.join($info_fields.split(','))
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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13 > '$output'
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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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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.
8bd645802765 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
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47 ]]></help>
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48 <expand macro="citations" />
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49 </tool>