Mercurial > repos > iuc > snpsift

annotate snpSift_vartype.xml @ 13:ed810da439cc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
author iuc
date Tue, 07 Jun 2016 09:41:13 -0400
parents b884686a80dc
children 80da7fae14b8
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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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1 <tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.0">
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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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b884686a80dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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6 <expand macro="requirements" />
b884686a80dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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7 <expand macro="stdio" />
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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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8 <expand macro="version_command" />
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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9 <command><![CDATA[
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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10 java -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" varType "$input" 2> "$log" > "$output"
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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11 ]]>
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12 </command>
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13 <inputs>
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14 <param format="vcf" name="input" type="data" label="Variant file (VCF)"/>
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15 </inputs>
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16 <outputs>
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17 <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" />
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18 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
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19 </outputs>
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20 <tests>
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21 </tests>
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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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22 <help><![CDATA[
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23 **What it does**
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24
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25 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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26
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27 .. _SnpSift Variant type: http://snpeff.sourceforge.net/SnpSift.html#VariantType
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28
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29 ------
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30
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31 **License**
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32
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33 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
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34
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35 .. _CRS4 Srl.: http://www.crs4.it/
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36 .. _MIT license: http://opensource.org/licenses/MIT
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37
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38 @CITATION_SECTION@
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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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40 ]]>
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41 </help>
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42 <expand macro="citations" />
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43 </tool>