Mercurial > repos > iuc > snpsift

annotate snpSift_vartype.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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bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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1 <tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.1">
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2 <description>Annotate with variant type</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" />
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9 <command><![CDATA[
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10 SnpSift varType
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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11 '$input'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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12 2> '$log'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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13 > '$output'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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14 ]]></command>
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15 <inputs>
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16 <param name="input" type="data" format="vcf" label="Variant file (VCF)"/>
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17 </inputs>
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18 <outputs>
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20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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19 <data name="output" format="vcf" label="${tool.name} on ${on_string}: VCF" />
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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20 <data name="log" format="txt" label="${tool.name} on ${on_string}: log" />
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21 </outputs>
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22 <tests>
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23 </tests>
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24 <help><![CDATA[
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25 **What it does**
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26
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27 This tool uses `SnpSift Variant type`_ to add the variant type (SNP/MNP/INS/DEL/MIXED) in the INFO field. It also adds "HOM/HET", but this last one works if there is only one sample (otherwise it doesn't make any sense).
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29 .. _SnpSift Variant type: http://snpeff.sourceforge.net/SnpSift.html#VariantType
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30
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31 ------
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32
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33 **License**
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34
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35 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
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36
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37 .. _CRS4 Srl.: http://www.crs4.it/
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38 .. _MIT license: https://opensource.org/licenses/MIT
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39 ]]></help>
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40 <expand macro="citations" />
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41 </tool>