Mercurial > repos > iuc > snpeff

comparison snpEff_databases.xml @ 29:ca2b512e8d7c draft default tip

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/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
author iuc
date Mon, 21 Oct 2024 13:56:15 +0000
parents 268d162b9c49
children
comparison
equal deleted inserted replaced
28:6322be79bd8e 29:ca2b512e8d7c
1 <tool id="snpEff_databases" name="SnpEff databases:" version="@WRAPPER_VERSION@.galaxy2"> 1 <tool id="snpEff_databases" name="SnpEff databases:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
2 <description> list available databases</description> 2 <description> list available databases</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>
15 | grep -e '^#' -e '${include_pattern}' 15 | grep -e '^#' -e '${include_pattern}'
16 #end if 16 #end if
17 17
18 #if $exclude_pattern: 18 #if $exclude_pattern:
19 | grep -v '${exclude_pattern}' 19 | grep -v '${exclude_pattern}'
20 #end if
21
22 #if str($include_download_path) == "no":
23 | cut -f 1,2,3,4
20 #end if 24 #end if
21 25
22 > '${snpeff_dbs}' 26 > '${snpeff_dbs}'
23 ]]></command> 27 ]]></command>
24 <inputs> 28 <inputs>
36 <add value="^" /> 40 <add value="^" />
37 <add value="_" /> 41 <add value="_" />
38 </valid> 42 </valid>
39 </sanitizer> 43 </sanitizer>
40 </param> 44 </param>
41 45 <param name="include_download_path" type="select" display="radio" label="Include download paths?" help="When snpEff dumps the list of available databases, it includes their download paths. These are not needed in the Galaxy context.">
46 <option value="yes">Yes</option>
47 <option value="no" selected="true">No</option>
48 </param>
42 </inputs> 49 </inputs>
43 <outputs> 50 <outputs>
44 <data name="snpeff_dbs" format="tabular" label="${tool.name} @SNPEFF_VERSION@ available databases" /> 51 <data name="snpeff_dbs" format="tabular" label="${tool.name} @SNPEFF_VERSION@ available databases" />
45 </outputs> 52 </outputs>
46 <tests> 53 <tests>
61 </test> 68 </test>
62 </tests> 69 </tests>
63 <help><![CDATA[ 70 <help><![CDATA[
64 **What it does** 71 **What it does**
65 72
66 This tool downloads the master list of snpEff databases from @SNPEFF_DATABASE_URL@. You can then look at this list and decide which database to use for your analysis. For example, if **List entries matching the following expression** parameter of this tool is set to *Mouse* the it will produce a tabular dataset with the following content:: 73 This tool downloads the master list of snpEff databases from a remote SnpEff repository. You can then look at this list and decide which database to use for your analysis. For example, if **List entries matching the following expression** parameter of this tool is set to *Mouse*, it will produce a tabular dataset with the following content::
67 74
68 mm10 Mouse http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_mm10.zip 75 mm10 Mouse
69 mm9 Mouse http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_mm9.zip 76 mm39 Mouse
77 mm9 Mouse
70 78
71 This means that there two available snpEff databases for mouse genome versions mm9 and mm10. In order to download these databases you should use identifier from the first column (e.g., mm9 or mm10 in this case). 79 This means that there are three available snpEff databases for mouse genome. If you want to use mm39 in you analysis:
80
81 - set **Genome source** option of **SnpEff eff** Galaxy tool to *Download on demand*
82 - enter 'mm39' into **Snpff Genome Version Name** text box
72 83
73 ------- 84 -------
74 85
75 .. class:: infomark 86 .. class:: infomark
76 87
81 #. Use **SnpEff download** tool. It will download the database to the history and you will be able to use it in **SnpEff eff** tool using *Downloaded snpEff database in your history* option of the **Genome source** parameter. 92 #. Use **SnpEff download** tool. It will download the database to the history and you will be able to use it in **SnpEff eff** tool using *Downloaded snpEff database in your history* option of the **Genome source** parameter.
82 #. Use *Download on demand* option of the **SnpEff eff** tool (again, **Genome source** parameter). In this case snpEff will download the database before performing annotation. 93 #. Use *Download on demand* option of the **SnpEff eff** tool (again, **Genome source** parameter). In this case snpEff will download the database before performing annotation.
83 94
84 @SNPEFF_IN_GALAXY_INFO@ 95 @SNPEFF_IN_GALAXY_INFO@
85 @EXTERNAL_DOCUMENTATION@ 96 @EXTERNAL_DOCUMENTATION@
97
86 ]]></help> 98 ]]></help>
87 <expand macro="citations" /> 99 <expand macro="citations" />
88 </tool> 100 </tool>
89 101