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comparison data_manager/data_manager_snpEff_download.xml @ 7:a6400027d849 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329
author iuc
date Tue, 24 Oct 2017 07:27:38 -0400
parents 3d9dd4b9fb09
children 08d7998c3afb
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6:2107b4f40945 7:a6400027d849
1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3k" tool_type="manage_data"> 1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3r" tool_type="manage_data">
2 <description>Download a new database</description> 2 <description>Download a new database</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.3k">snpeff</requirement> 4 <requirement type="package" version="4.3.1r">snpeff</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 python '$__tool_directory__/data_manager_snpEff_download.py' 7 python '$__tool_directory__/data_manager_snpEff_download.py'
8 --genome_version '$genome_version' 8 --genome_version '$genome_version'
9 '$out_file' 9 '$out_file'
23 <output name="out_file"> 23 <output name="out_file">
24 <assert_contents> 24 <assert_contents>
25 <!-- Check that a genome was added --> 25 <!-- Check that a genome was added -->
26 <has_text text="GRCh38.76" /> 26 <has_text text="GRCh38.76" />
27 <has_text text="snpeffv_regulationdb" /> 27 <has_text text="snpeffv_regulationdb" />
28 <has_text text="snpeffv_annotations" />
29 </assert_contents> 28 </assert_contents>
30 </output> 29 </output>
31 </test> 30 </test>
32 </tests> 31 </tests>
33 <help><![CDATA[ 32 <help><![CDATA[
34 This tool downloads a SnpEff database and populates the data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations. 33 This tool downloads a SnpEff database and populates the data tables: snpeffv_genomedb, snpeffv_regulationdb.
35 34
36 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 35 To see the list of available SnpEff genomes, run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeffv_databases.
37 36
38 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/ 37 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/
39 38
40 For details about this tool, please go to http://snpeff.sourceforge.net 39 For details about this tool, please go to http://snpeff.sourceforge.net
41 ]]></help> 40 ]]></help>