Mercurial > repos > iuc > snpeff

annotate 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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
29
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
1 <tool id="snpEff_databases" name="SnpEff databases:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
2 <description> list available databases</description>
1
500832f27cbc Uploaded
iuc
parents:
diff changeset
3 <macros>
500832f27cbc Uploaded
iuc
parents:
diff changeset
4 <import>snpEff_macros.xml</import>
500832f27cbc Uploaded
iuc
parents:
diff changeset
5 </macros>
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
6 <requirements>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
7 <expand macro="requirement" />
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
8 </requirements>
3
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
9 <expand macro="stdio" />
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
10 <expand macro="version_command" />
7
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
iuc
parents: 4
diff changeset
11 <command><![CDATA[
12
5a29ab10dba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents: 10
diff changeset
12 snpEff databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g'
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
13
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
14 #if $include_pattern:
22
268d162b9c49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 02789207093cd84eaa6550149869c16b257d093b"
iuc
parents: 17
diff changeset
15 | grep -e '^#' -e '${include_pattern}'
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
16 #end if
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
17
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
18 #if $exclude_pattern:
12
5a29ab10dba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents: 10
diff changeset
19 | grep -v '${exclude_pattern}'
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
20 #end if
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
21
29
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
22 #if str($include_download_path) == "no":
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
23 | cut -f 1,2,3,4
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
24 #end if
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
25
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
26 > '${snpeff_dbs}'
7
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
iuc
parents: 4
diff changeset
27 ]]></command>
1
500832f27cbc Uploaded
iuc
parents:
diff changeset
28 <inputs>
17
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
iuc
parents: 16
diff changeset
29 <param name="include_pattern" type="text" value="" optional="true" label="List entries matching the following expression" help="Databases matching this expression will be listed. Here you can enter text or regular expression. For example, to show only mouse databases use 'Mouse'. Note that this parameter is case-sensitive.">
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
30 <sanitizer>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
31 <valid initial="string.digits,string.letters">
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
32 <add value="^" />
16
c9ecd2a96ecf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 33017565e3dd788161910bd856aff43fbb57a58f
iuc
parents: 12
diff changeset
33 <add value="_" />
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
34 </valid>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
35 </sanitizer>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
36 </param>
17
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
iuc
parents: 16
diff changeset
37 <param name="exclude_pattern" type="text" value="" optional="true" label="Do not output entries matching the following expression" help="Databases matching this expression WILL NOT BE listed. Here you can enter text or regular expression. For excample, to avoid all ENSEMBL bundles enter 'ENSEMBL'. Note that this parameter is case-sensitive.">
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
38 <sanitizer>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
39 <valid initial="string.digits,string.letters">
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
40 <add value="^" />
16
c9ecd2a96ecf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 33017565e3dd788161910bd856aff43fbb57a58f
iuc
parents: 12
diff changeset
41 <add value="_" />
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
42 </valid>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
43 </sanitizer>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
44 </param>
29
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
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.">
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
46 <option value="yes">Yes</option>
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
47 <option value="no" selected="true">No</option>
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
48 </param>
1
500832f27cbc Uploaded
iuc
parents:
diff changeset
49 </inputs>
500832f27cbc Uploaded
iuc
parents:
diff changeset
50 <outputs>
17
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
iuc
parents: 16
diff changeset
51 <data name="snpeff_dbs" format="tabular" label="${tool.name} @SNPEFF_VERSION@ available databases" />
1
500832f27cbc Uploaded
iuc
parents:
diff changeset
52 </outputs>
3
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
53 <tests>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
54 <test>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
55 <output name="snpeff_dbs">
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
56 <assert_contents>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
57 <has_text text="ebola_zaire" />
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
58 </assert_contents>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
59 </output>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
60 </test>
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
61 <test>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
62 <param name="include_pattern" value="ebola"/>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
63 <output name="snpeff_dbs">
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
64 <assert_contents>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
65 <has_text text="ebola_zaire" />
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
66 </assert_contents>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
67 </output>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
68 </test>
3
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
69 </tests>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
70 <help><![CDATA[
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
71 **What it does**
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
72
29
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
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::
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
74
29
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
75 mm10 Mouse
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
76 mm39 Mouse
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
77 mm9 Mouse
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
78
29
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
79 This means that there are three available snpEff databases for mouse genome. If you want to use mm39 in you analysis:
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
80
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
81 - set **Genome source** option of **SnpEff eff** Galaxy tool to *Download on demand*
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
82 - enter 'mm39' into **Snpff Genome Version Name** text box
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
83
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
84 -------
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
85
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
86 .. class:: infomark
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
87
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
88 **The usage scenario**
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
89
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
90 There are two ways to use names of databases obtained with this tool in Galaxy's version on snpEff:
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
91
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
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.
12
5a29ab10dba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents: 10
diff changeset
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.
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
94
17
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
iuc
parents: 16
diff changeset
95 @SNPEFF_IN_GALAXY_INFO@
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
iuc
parents: 16
diff changeset
96 @EXTERNAL_DOCUMENTATION@
29
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
iuc
parents: 22
diff changeset
97
7
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
iuc
parents: 4
diff changeset
98 ]]></help>
3
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
99 <expand macro="citations" />
1
500832f27cbc Uploaded
iuc
parents:
diff changeset
100 </tool>
500832f27cbc Uploaded
iuc
parents:
diff changeset
101