Mercurial > repos > iuc > data_manager_snpeff

annotate data_manager/data_manager_snpEff_download.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_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0" tool_type="manage_data">
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2 <description>Download a new database</description>
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3 <macros>
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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" />
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9 <command><![CDATA[
e5a471c4630e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
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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 $__tool_directory__/data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
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12 --genome_version "$genome_version" "$out_file"
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13 ]]>
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14 </command>
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15 <inputs>
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16 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
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17 <help>https://snpeff-data.galaxyproject.org/databases/</help>
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18 <validator type="regex" message="A genome version name is required">\S+</validator>
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19 </param>
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20 </inputs>
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22 <outputs>
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23 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
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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="genome_version" value="GRCh38.76"/>
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28 <output name="out_file">
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29 <assert_contents>
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30 <!-- Check that a genome was added -->
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31 <has_text text="GRCh38.76" />
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32 <has_text text="snpeffv_regulationdb" />
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33 <has_text text="snpeffv_annotations" />
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34 </assert_contents>
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35 </output>
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36 </test>
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37 </tests>
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38 <help>
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39
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40 This tool downloads a SnpEff database and populates data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations.
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41
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85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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42 To see the list of available SnpEff genomes run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeff4_databases
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44 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/
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47 For details about this tool, please go to http://snpEff.sourceforge.net
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48
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49 Please cite:
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50 "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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52 </help>
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53 <expand macro="citations" />
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54 </tool>
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