Mercurial > repos > iuc > snpeff
comparison snpEff_download.xml @ 12:5a29ab10dba6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
| author | iuc |
|---|---|
| date | Thu, 29 Mar 2018 20:39:49 -0400 |
| parents | 5b4ac70948d2 |
| children | 65ae79bddc69 |
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| 11:bfa6c1b8a03c | 12:5a29ab10dba6 |
|---|---|
| 1 <tool id="snpEff_download" name="SnpEff download:" version="@wrapper_version@.1"> | 1 <tool id="snpEff_download" name="SnpEff download:" version="@wrapper_version@.galaxy1"> |
| 2 <description> download a pre-built database</description> | 2 <description> download a pre-built database</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>snpEff_macros.xml</import> | 4 <import>snpEff_macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <requirements> | 6 <requirements> |
| 32 </tests> | 32 </tests> |
| 33 <help><![CDATA[ | 33 <help><![CDATA[ |
| 34 | 34 |
| 35 **What it does** | 35 **What it does** |
| 36 | 36 |
| 37 This tool downloads a specified database from @snpeff_database_url@. It deposits it into the history. | 37 This tool downloads a specified database from @snpeff_database_url@. It deposits it into the history. |
| 38 | 38 |
| 39 ------- | 39 ------- |
| 40 | 40 |
| 41 .. class:: infomark | 41 .. class:: infomark |
| 42 | 42 |
| 44 | 44 |
| 45 Suppose you want to annoate a VCF file containing variants within mm10 version of the Mouse genome. To do this you can: | 45 Suppose you want to annoate a VCF file containing variants within mm10 version of the Mouse genome. To do this you can: |
| 46 | 46 |
| 47 #. Download mm10 snpEff database by typing *mm10* into **Select the annotation database...** text box. | 47 #. Download mm10 snpEff database by typing *mm10* into **Select the annotation database...** text box. |
| 48 #. Use **SnpEff eff** by choosing the downloaded database from the history using *Downloaded snpEff database in your history* option of the **Genome source** parameter. | 48 #. Use **SnpEff eff** by choosing the downloaded database from the history using *Downloaded snpEff database in your history* option of the **Genome source** parameter. |
| 49 | 49 |
| 50 @snpeff_in_galaxy_info@ | 50 @snpeff_in_galaxy_info@ |
| 51 @external_documentation@ | 51 @external_documentation@ |
| 52 ]]></help> | 52 ]]></help> |
| 53 <expand macro="citations" /> | 53 <expand macro="citations" /> |
| 54 </tool> | 54 </tool> |