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comparison data_manager/data_manager_snpEff_download.xml @ 0:111fc9457ec6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
author iuc
date Tue, 07 Jun 2016 10:13:35 -0400
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1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.1.0" tool_type="manage_data">
2 <description>Download a new database</description>
3 <requirements>
4 <requirement type="package" version="4.1">snpEff</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
8 <exit_code range="1:" level="fatal" description="Error" />
9 </stdio>
10 <command interpreter="python">
11 data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
12 --genome_version "$genome_version" "$out_file"
13 </command>
14 <inputs>
15 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
16 <help>https://snpeff-data.galaxyproject.org/databases/</help>
17 <validator type="regex" message="A genome version name is required">\S+</validator>
18 </param>
19 </inputs>
20
21 <outputs>
22 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
23 </outputs>
24 <tests>
25 <test>
26 <param name="genome_version" value="GRCh38.76"/>
27 <output name="out_file">
28 <assert_contents>
29 <!-- Check that a genome was added -->
30 <has_text text="GRCh38.76" />
31 <has_text text="snpeffv_regulationdb" />
32 <has_text text="snpeffv_annotations" />
33 </assert_contents>
34 </output>
35 </test>
36 </tests>
37 <help>
38
39 This tool downloads a SnpEff database and populates data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations.
40
41 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
42
43 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/
44
45
46 For details about this tool, please go to http://snpEff.sourceforge.net
47
48 Please cite:
49 "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]
50
51 </help>
52 <citations>
53 <citation type="doi">10.4161/fly.19695</citation>
54 </citations>
55 </tool>
56