Mercurial > repos > iuc > data_manager_snpeff
comparison data_manager/data_manager_snpEff_download.xml @ 1:85a23e2dd92b draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
author | iuc |
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date | Tue, 07 Jun 2016 10:11:50 -0400 |
parents | 9ac823a8b328 |
children | e5a471c4630e |
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0:9ac823a8b328 | 1:85a23e2dd92b |
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1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.0.0" tool_type="manage_data"> | 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> | 2 <description>Download a new database</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="4.0">snpEff</requirement> | 4 <requirement type="package" version="4.1">snpEff</requirement> |
5 </requirements> | 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> | |
6 <command interpreter="python"> | 10 <command interpreter="python"> |
7 data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config | 11 data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config" |
8 --genome_version "$genome_version" "$out_file" | 12 --genome_version "$genome_version" "$out_file" |
9 </command> | 13 </command> |
10 <inputs> | 14 <inputs> |
11 <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> | 15 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> |
12 <help>https://snpeff-data.galaxyproject.org/databases/</help> | 16 <help>https://snpeff-data.galaxyproject.org/databases/</help> |
13 <validator type="regex" message="A genome version name is required">\S+</validator> | 17 <validator type="regex" message="A genome version name is required">\S+</validator> |
14 </param> | 18 </param> |
15 </inputs> | 19 </inputs> |
16 | 20 |
17 <outputs> | 21 <outputs> |
18 <data name="out_file" format="data_manager_json" label="${tool.name}"/> | 22 <data name="out_file" format="data_manager_json" label="${tool.name}"/> |
19 </outputs> | 23 </outputs> |
20 <stdio> | |
21 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
22 <exit_code range="1:" level="fatal" description="Error" /> | |
23 </stdio> | |
24 <tests> | 24 <tests> |
25 <test> | 25 <test> |
26 <param name="genome_version" value="GRCh38.76"/> | 26 <param name="genome_version" value="GRCh38.76"/> |
27 <output name="out_file"> | 27 <output name="out_file"> |
28 <assert_contents> | 28 <assert_contents> |
36 </tests> | 36 </tests> |
37 <help> | 37 <help> |
38 | 38 |
39 This tool downloads a SnpEff database and populates 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 | 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 | 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 | 42 |
43 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/ | 43 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/ |
44 | 44 |
45 | 45 |
46 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 |
47 | 47 |
48 Please cite: | 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] | 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 | 50 |
51 </help> | 51 </help> |
52 <citations> | |
53 <citation type="doi">10.4161/fly.19695</citation> | |
54 </citations> | |
52 </tool> | 55 </tool> |
53 | 56 |