Mercurial > repos > iuc > snpeff_sars_cov_2

comparison snpEff_macros.xml @ 0:2a3a00c1fa0a draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e6d1b32be9df14beb1e2859a0d2fa29a2d09227e"
author iuc
date Thu, 18 Jun 2020 16:11:49 -0400
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-1:000000000000 0:2a3a00c1fa0a
1 <macros>
2 <xml name="requirement">
3 <requirement type="package" version="4.5covid19">snpeff</requirement>
4 <yield/>
5 </xml>
6 <xml name="stdio">
7 <stdio>
8 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
9 <exit_code range="1:" level="fatal" description="Error" />
10 </stdio>
11 </xml>
12 <xml name="version_command">
13 <version_command><![CDATA[
14 snpEff -version
15 ]]></version_command>
16 </xml>
17 <token name="@WRAPPER_VERSION@">4.5covid19</token>
18 <token name="@SNPEFF_VERSION@">SnpEff4.5</token>
19 <token name="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token>
20 <token name="@EXTERNAL_DOCUMENTATION@">
21
22
23 -------
24
25 To learn more about SnpEff read its manual at http://snpeff.sourceforge.net/SnpEff_manual.html
26 </token>
27 <token name="@SNPEFF_IN_GALAXY_INFO@">
28
29 -------
30
31 .. class:: warningmark
32
33 **Databases in the SnpEff Covid-19 edition**
34
35 This special version of SnpEff provides only a fixed number of
36 SARS-CoV-2-related genome databases.
37
38 Unlike with regular SnpEff releases, it is not possible to extend this set,
39 *i.e*, you cannot download additional databases or build custom databases for
40 this edition.
41 </token>
42
43
44
45 <xml name="citations">
46 <citations>
47 <citation type="doi">10.4161/fly.19695</citation>
48 <yield />
49 </citations>
50 </xml>
51 </macros>