Mercurial > repos > iuc > snpeff

annotate snpEff_macros.xml @ 3:b24873564cf6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
author iuc
date Tue, 07 Jun 2016 10:03:17 -0400
parents 500832f27cbc
children 698ef30638a8
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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4 <requirement type="package" version="4.1">snpEff</requirement>
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5 </requirements>
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6 </xml>
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7 <xml name="stdio">
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8 <stdio>
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9 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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10 <exit_code range="1:" level="fatal" description="Error" />
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11 </stdio>
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12 </xml>
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b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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13 <xml name="version_command">
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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14 <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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15 </xml>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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16 <token name="@WRAPPER_VERSION@">4.1</token>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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17 <token name="@SNPEFF_VERSION@">SnpEff4.1</token>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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18 <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_1/</token>
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19 <token name="@EXTERNAL_DOCUMENTATION@">
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21 For details about this tool, please go to:
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22 http://snpeff.sourceforge.net/SnpEff_manual.html
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24 </token>
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25 <token name="@CITATION_SECTION@">------
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27 **Citation**
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29 For the underlying tool, please cite the following two publications:
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31 SnpEff citation:
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32 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly 6(2):80-92, 2012
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34 </token>
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35 <xml name="citations">
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36 <citations>
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37 <citation type="doi">10.4161/fly.19695</citation>
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38 <yield />
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39 </citations>
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40 </xml>
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41 </macros>