Mercurial > repos > iuc > data_manager_snpeff

annotate data_manager/data_manager_snpEff_download.xml @ 5:3d9dd4b9fb09 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 09:40:03 -0400
parents 847b0f43c0e5
children a6400027d849
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3k" tool_type="manage_data">
0
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
2 <description>Download a new database</description>
4
847b0f43c0e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 3
diff changeset
3 <requirements>
5
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
4 <requirement type="package" version="4.3k">snpeff</requirement>
4
847b0f43c0e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 3
diff changeset
5 </requirements>
5
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
7 python '$__tool_directory__/data_manager_snpEff_download.py'
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
8 --genome_version '$genome_version'
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
9 '$out_file'
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
10 ]]></command>
0
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
11 <inputs>
5
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
12 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)" help="https://snpeff-data.galaxyproject.org/databases/">
0
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
13 <validator type="regex" message="A genome version name is required">\S+</validator>
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
14 </param>
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
15 </inputs>
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
16
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
17 <outputs>
5
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
18 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
0
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
19 </outputs>
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
20 <tests>
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
21 <test>
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
22 <param name="genome_version" value="GRCh38.76"/>
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
23 <output name="out_file">
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
24 <assert_contents>
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
25 <!-- Check that a genome was added -->
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
26 <has_text text="GRCh38.76" />
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
27 <has_text text="snpeffv_regulationdb" />
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
28 <has_text text="snpeffv_annotations" />
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
29 </assert_contents>
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
30 </output>
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
31 </test>
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
32 </tests>
5
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
33 <help><![CDATA[
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
34 This tool downloads a SnpEff database and populates the data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations.
0
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
35
1
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents: 0
diff changeset
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
0
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
37
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
38 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
39
5
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
40 For details about this tool, please go to http://snpeff.sourceforge.net
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
41 ]]></help>
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
42 <citations>
4
847b0f43c0e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 3
diff changeset
43 <citation type="doi">10.4161/fly.19695</citation>
5
3d9dd4b9fb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 4
diff changeset
44 </citations>
0
9ac823a8b328 Uploaded
iuc
parents:
diff changeset
45 </tool>