Mercurial > repos > iuc > data_manager_snpeff

annotate data_manager/data_manager_snpEff_databases.xml @ 3:e5a471c4630e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
author iuc
date Mon, 31 Oct 2016 08:13:11 -0400
parents 85a23e2dd92b
children 847b0f43c0e5
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e5a471c4630e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
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1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="@WRAPPER_VERSION@.0" tool_type="manage_data">
e5a471c4630e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
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2 <description>Read the list of available snpEff databases</description>
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3 <macros>
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iuc
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4 <import>snpEff_macros.xml</import>
e5a471c4630e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
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5 </macros>
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6 <expand macro="requirements" />
e5a471c4630e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
e5a471c4630e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
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9 <command><![CDATA[
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10 @CONDA_SNPEFF_JAR_PATH@ &&
e5a471c4630e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
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11 python '$__tool_directory__/data_manager_snpEff_databases.py'
e5a471c4630e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
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12 --jar_path '\$SNPEFF_JAR_PATH/snpEff.jar'
e5a471c4630e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
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13 '$out_file'
e5a471c4630e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
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14 ]]>
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15 </command>
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16 <inputs>
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17 </inputs>
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18 <outputs>
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19 <data name="out_file" format="data_manager_json"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <output name="out_file">
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24 <assert_contents>
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25 <!-- Check that a genome was added -->
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26 <has_text text="GRCh38.76" />
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27 </assert_contents>
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28 </output>
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29 </test>
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30 </tests>
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31 <help>
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32
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33 This tool updatess the list of SnpEff databases for the SnpEff Download data manager.
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34 It should only need to be run once for a snpEff version,
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35 since it populates the SnpEff Download data manager from the snpEff config file.
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36
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37 For information about snpEff: http://snpEff.sourceforge.net
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39 Please cite:
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40 "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 (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
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e5a471c4630e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
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42 </help>
e5a471c4630e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
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43 <expand macro="citations" />
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44 </tool>
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