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comparison data_manager/data_manager_snpEff_download.xml @ 4:a9cace1ee2b7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
author iuc
date Tue, 18 Apr 2017 09:39:00 -0400
parents 821c34cdacb6
children a6e6e8415b7f
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3:821c34cdacb6 4:a9cace1ee2b7
1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.1.0" tool_type="manage_data"> 1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3k" 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="4.1">snpEff</requirement> 4 <requirement type="package" version="4.3k">snpeff</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <command detect_errors="exit_code"><![CDATA[
7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> 7 python '$__tool_directory__/data_manager_snpEff_download.py'
8 <exit_code range="1:" level="fatal" description="Error" /> 8 --genome_version '$genome_version'
9 </stdio> 9 '$out_file'
10 <command interpreter="python"> 10 ]]></command>
11 data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
12 --genome_version "$genome_version" "$out_file"
13 </command>
14 <inputs> 11 <inputs>
15 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> 12 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)" help="https://snpeff-data.galaxyproject.org/databases/">
16 <help>https://snpeff-data.galaxyproject.org/databases/</help>
17 <validator type="regex" message="A genome version name is required">\S+</validator> 13 <validator type="regex" message="A genome version name is required">\S+</validator>
18 </param> 14 </param>
19 </inputs> 15 </inputs>
20 16
21 <outputs> 17 <outputs>
22 <data name="out_file" format="data_manager_json" label="${tool.name}"/> 18 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
23 </outputs> 19 </outputs>
24 <tests> 20 <tests>
25 <test> 21 <test>
26 <param name="genome_version" value="GRCh38.76"/> 22 <param name="genome_version" value="GRCh38.76"/>
27 <output name="out_file"> 23 <output name="out_file">
32 <has_text text="snpeffv_annotations" /> 28 <has_text text="snpeffv_annotations" />
33 </assert_contents> 29 </assert_contents>
34 </output> 30 </output>
35 </test> 31 </test>
36 </tests> 32 </tests>
37 <help> 33 <help><![CDATA[
38 34 This tool downloads a SnpEff database and populates the data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations.
39 This tool downloads a SnpEff database and populates data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations.
40 35
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 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
42 37
43 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/ 38 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/
44 39
45 40 For details about this tool, please go to http://snpeff.sourceforge.net
46 For details about this tool, please go to http://snpEff.sourceforge.net 41 ]]></help>
47 42 <citations>
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> 43 <citation type="doi">10.4161/fly.19695</citation>
54 </citations> 44 </citations>
55 </tool> 45 </tool>
56