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comparison snpEff_download.xml @ 10:5b4ac70948d2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
author iuc
date Tue, 27 Mar 2018 09:44:18 -0400
parents 68693743661e
children 5a29ab10dba6
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9:68693743661e 10:5b4ac70948d2
1 <tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.1"> 1 <tool id="snpEff_download" name="SnpEff download:" version="@wrapper_version@.1">
2 <description>Download a new 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 <expand macro="requirements" /> 6 <requirements>
7 <expand macro="requirement" />
8 </requirements>
7 <expand macro="stdio" /> 9 <expand macro="stdio" />
8 <expand macro="version_command" /> 10 <expand macro="version_command" />
9 <command><![CDATA[ 11 <command><![CDATA[
10 snpEff download -dataDir '$snpeff_db.files_path' -v '$genome_version' 12 snpEff download -dataDir '$snpeff_db.files_path' -v '$genome_version'
11 ]]></command> 13 ]]></command>
12 <inputs> 14 <inputs>
13 <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh38.86, GRCh37.75, hg38, or GRCm38.86)"> 15 <param name="genome_version" type="text" value="" label="Select the annotation database you want to download (e.g. GRCh38.86, mm10 etc.)" help="The list of available databases can be obtained with 'SnpEff databases' tool">
14 <help>@SNPEFF_DATABASE_URL@</help> 16 <help>@snpeff_database_url@</help>
15 <validator type="regex" message="A genome version name is required">\S+</validator> 17 <validator type="regex" message="A genome version name is required">\S+</validator>
16 </param> 18 </param>
17 </inputs> 19 </inputs>
18 <outputs> 20 <outputs>
19 <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" /> 21 <data format="snpeffdb" name="snpeff_db" label="${tool.name} @snpeff_version@ ${genome_version}"/>
20 </outputs> 22 </outputs>
21 <tests> 23 <tests>
22 <test> 24 <test>
23 <param name="genome_version" value="ebola_zaire"/> 25 <param name="genome_version" value="ebola_zaire"/>
24 <output name="snpeff_db"> 26 <output name="snpeff_db">
27 </assert_contents> 29 </assert_contents>
28 </output> 30 </output>
29 </test> 31 </test>
30 </tests> 32 </tests>
31 <help><![CDATA[ 33 <help><![CDATA[
32 @EXTERNAL_DOCUMENTATION@ 34
35 **What it does**
36
37 This tool downloads a specified database from @snpeff_database_url@. It deposits it into the history.
38
39 -------
40
41 .. class:: infomark
42
43 **The usage scenario**
44
45 Suppose you want to annoate a VCF file containing variants within mm10 version of the Mouse genome. To do this you can:
46
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.
49
50 @snpeff_in_galaxy_info@
51 @external_documentation@
33 ]]></help> 52 ]]></help>
34 <expand macro="citations" /> 53 <expand macro="citations" />
35 </tool> 54 </tool>