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comparison snpEff_macros.xml @ 29:ca2b512e8d7c draft default tip

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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 5c7b70713fb5
children
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28:6322be79bd8e 29:ca2b512e8d7c
1 <macros> 1 <macros>
2 <xml name="requirement"> 2 <xml name="requirement">
3 <requirement type="package" version="4.3.1t">snpeff</requirement> 3 <requirement type="package" version="5.2">snpeff</requirement>
4 <yield/> 4 <yield/>
5 </xml> 5 </xml>
6 <xml name="stdio"> 6 <xml name="stdio">
7 <stdio> 7 <stdio>
8 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> 8 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
12 <xml name="version_command"> 12 <xml name="version_command">
13 <version_command><![CDATA[ 13 <version_command><![CDATA[
14 snpEff -version 14 snpEff -version
15 ]]></version_command> 15 ]]></version_command>
16 </xml> 16 </xml>
17 <token name="@WRAPPER_VERSION@">4.3+T</token> 17 <token name="@WRAPPER_VERSION@">0</token>
18 <token name="@SNPEFF_VERSION@">SnpEff4.3</token> 18 <token name="@SNPEFF_VERSION@">5.2</token>
19 <token name="@SNPEFF_DATABASE_URL@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token>
20 <token name="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token> 19 <token name="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token>
21 <xml name="ref_select"> 20 <xml name="ref_select">
22 <conditional name="reference_source"> 21 <conditional name="reference_source">
23 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> 22 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
24 <option value="cached">Locally cached</option> 23 <option value="cached">Locally cached</option>
57 56
58 In you *do not see them* keep reading... 57 In you *do not see them* keep reading...
59 58
60 **Download pre-built databases** 59 **Download pre-built databases**
61 60
62 SnpEff project generates large numbers of pre-build databases. These are available at @SNPEFF_DATABASE_URL@ and can downloaded. Follow these steps: 61 SnpEff project generates large numbers of pre-build databases. To obtain and use them follow these steps:
63 62
64 #. Use **SnpEff databases** tool to generate a list of existing databases. Note the name of the database you need. 63 #. Use **SnpEff databases** tool to generate a list of existing databases. Note the name of the database you need.
65 #. Use **SnpEff download** tool to download the database. 64 #. Use **SnpEff download** tool to download the database.
66 #. Finally, use **SnpEff eff** by choosing the downloaded database from the history using *Downloaded snpEff database in your history* option of the **Genome source** parameter. 65 #. Finally, use **SnpEff eff** by choosing the downloaded database from the history using *Downloaded snpEff database in your history* option of the **Genome source** parameter.
67 66