Mercurial > repos > iuc > data_manager_snpeff
comparison data_manager/data_manager_snpEff_download.xml @ 5:3d9dd4b9fb09 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
author | iuc |
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date | Tue, 18 Apr 2017 09:40:03 -0400 |
parents | 847b0f43c0e5 |
children | a6400027d849 |
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4:847b0f43c0e5 | 5:3d9dd4b9fb09 |
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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 |