Mercurial > repos > sh477 > data_manager_vep_cache_downloader
comparison data_manager/data_manager_vep_cache_download.xml @ 7:7890790d2afd draft
Fully working now and improved several things
author | sh477 |
---|---|
date | Tue, 01 Mar 2022 18:12:26 +0000 |
parents | a3dba0440f08 |
children | 3f3246b8972e |
comparison
equal
deleted
inserted
replaced
6:3bd006fa2be2 | 7:7890790d2afd |
---|---|
9 <inputs> | 9 <inputs> |
10 <param name="dbkey" type="genomebuild" | 10 <param name="dbkey" type="genomebuild" |
11 label="DBKEY of genome that the VEP cache data is for" | 11 label="DBKEY of genome that the VEP cache data is for" |
12 help="" /> | 12 help="" /> |
13 <param name="url" type="text" value="http://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/" | 13 <param name="url" type="text" value="http://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/" |
14 label="FTP root url for VEP cache files" help=""/> | 14 label="FTP root url for VEP cache files" help="Release number should be equal to desired VEP version"/> |
15 <param name="file_name" type="text" label="File name of cache file to be downloaded from root url." help="E.g. homo_sapiens_vep_105_GRCh38.tar.gz"/> | 15 <param name="file_name" type="text" label="File name of cache file to be downloaded from root url" help="E.g. homo_sapiens_vep_105_GRCh38.tar.gz"/> |
16 <param name="display_name" type="text" label="Display name used in data-selection dropdowns." help="E.g. Homo sapiens hg38 (V105)"/> | |
17 </inputs> | 16 </inputs> |
18 <outputs> | 17 <outputs> |
19 <data name="out_file" format="data_manager_json"/> | 18 <data name="out_file" format="data_manager_json"/> |
20 </outputs> | 19 </outputs> |
21 <tests> | 20 <tests> |
22 <test> | 21 <test> |
23 <param name="dbkey" value="ce11"/> | 22 <param name="dbkey" value="ci3"/> |
24 <param name="url" value="http://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/"/> | 23 <param name="url" value="http://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/"/> |
25 <param name="file_name" value="caenorhabditis_elegans_vep_105_WBcel235.tar.gz"/> | 24 <param name="file_name" value="ciona_intestinalis_refseq_vep_105_KH.tar.gz"/> |
26 <param name="display_name" value="C. elegans ce11 (V105)"/> | |
27 <output name="out_file" file="from_test-meta.data_manager.json"/> | 25 <output name="out_file" file="from_test-meta.data_manager.json"/> |
28 </test> | 26 </test> |
29 </tests> | 27 </tests> |
30 <help> | 28 <help> |
31 This tool downloads given versions of VEP cache annotation files and makes them available to Ensembl VEP in Galaxy via the | 29 This tool downloads given versions of VEP cache annotation files and makes them available to Ensembl VEP in Galaxy via the |
32 "vep_versioned_caches" data table. You should use the indexed version of the cache files and it is strongly recommended to | 30 "vep_versioned_annotation_cache" data table. You should use the indexed version of the cache files and it is strongly |
33 use the cache files which version number matches the VEP version number. Note that for most genomes there are three versions | 31 recommended to use the cache files which version number matches the VEP version number. Note that for most genomes there |
34 of cache data available: default, refseq and merged (combining the former two). Choose the one suitable for your usage. | 32 are three versions of cache data available: default, refseq and merged (combining the former two). Choose the one suitable |
33 for your usage. | |
35 | 34 |
36 A general introduction to the VEP cache and download links can be found on the official website: | 35 A general introduction to the VEP cache and download links can be found on the official website: |
37 https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html | 36 https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html |
38 </help> | 37 </help> |
39 <citations> | 38 <citations> |