Mercurial > repos > iuc > data_manager_snpeff
comparison data_manager/data_manager_snpEff_download.xml @ 6:a6e6e8415b7f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329
| author | iuc |
|---|---|
| date | Tue, 24 Oct 2017 07:26:43 -0400 |
| parents | a9cace1ee2b7 |
| children | fbb459120c29 |
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| 5:87f6cff1bd43 | 6:a6e6e8415b7f |
|---|---|
| 1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3k" tool_type="manage_data"> | 1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3r" 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="4.3k">snpeff</requirement> | 4 <requirement type="package" version="4.3.1r">snpeff</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
| 7 python '$__tool_directory__/data_manager_snpEff_download.py' | 7 python '$__tool_directory__/data_manager_snpEff_download.py' |
| 8 --genome_version '$genome_version' | 8 --genome_version '$genome_version' |
| 9 '$out_file' | 9 '$out_file' |
| 23 <output name="out_file"> | 23 <output name="out_file"> |
| 24 <assert_contents> | 24 <assert_contents> |
| 25 <!-- Check that a genome was added --> | 25 <!-- Check that a genome was added --> |
| 26 <has_text text="GRCh38.76" /> | 26 <has_text text="GRCh38.76" /> |
| 27 <has_text text="snpeffv_regulationdb" /> | 27 <has_text text="snpeffv_regulationdb" /> |
| 28 <has_text text="snpeffv_annotations" /> | |
| 29 </assert_contents> | 28 </assert_contents> |
| 30 </output> | 29 </output> |
| 31 </test> | 30 </test> |
| 32 </tests> | 31 </tests> |
| 33 <help><![CDATA[ | 32 <help><![CDATA[ |
| 34 This tool downloads a SnpEff database and populates the data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations. | 33 This tool downloads a SnpEff database and populates the data tables: snpeffv_genomedb, snpeffv_regulationdb. |
| 35 | 34 |
| 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 | 35 To see the list of available SnpEff genomes, run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeffv_databases. |
| 37 | 36 |
| 38 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/ | 37 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/ |
| 39 | 38 |
| 40 For details about this tool, please go to http://snpeff.sourceforge.net | 39 For details about this tool, please go to http://snpeff.sourceforge.net |
| 41 ]]></help> | 40 ]]></help> |