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comparison data_manager/data_manager_snpEff_databases.xml @ 0:9ac823a8b328 draft

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author iuc
date Thu, 22 Jan 2015 09:14:50 -0500
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1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.0.0" tool_type="manage_data">
2 <description>Read the list of available snpEff databases</description>
3 <requirements>
4 <requirement type="package" version="4.0">snpEff</requirement>
5 </requirements>
6 <command interpreter="python">
7 data_manager_snpEff_databases.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar "$out_file"
8 </command>
9 <inputs>
10 </inputs>
11 <outputs>
12 <data name="out_file" format="data_manager_json"/>
13 </outputs>
14 <stdio>
15 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
16 <exit_code range="1:" level="fatal" description="Error" />
17 </stdio>
18 <tests>
19 <test>
20 <output name="out_file">
21 <assert_contents>
22 <!-- Check that a genome was added -->
23 <has_text text="GRCh38.76" />
24 </assert_contents>
25 </output>
26 </test>
27 </tests>
28 <help>
29
30 This tool updatess the list of SnpEff databases for the SnpEff Download data manager.
31 It should only need to be run once for a snpEff version,
32 since it populates the SnpEff Download data manager from the snpEff config file.
33
34 For information about snpEff: http://snpEff.sourceforge.net
35
36 Please cite:
37 "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]
38
39 </help>
40 </tool>
41