Mercurial > repos > iuc > snpeff

annotate snpEff_databases.xml @ 16:7c4ede6d88a2 draft

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 a69e15a4016b3088ec937d6f2349be091c6b1b71
author iuc
date Thu, 29 Mar 2018 20:39:33 -0400
parents a7c106b938dd
children 282a9b14496f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
16
7c4ede6d88a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents: 14
diff changeset
1 <tool id="snpEff_databases" name="SnpEff databases:" version="@wrapper_version@.galaxy1">
14
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
2 <description> list available databases</description>
2
114f423f99c0 Uploaded
iuc
parents:
diff changeset
3 <macros>
114f423f99c0 Uploaded
iuc
parents:
diff changeset
4 <import>snpEff_macros.xml</import>
114f423f99c0 Uploaded
iuc
parents:
diff changeset
5 </macros>
14
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
6 <requirements>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
7 <expand macro="requirement" />
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
8 </requirements>
5
92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 2
diff changeset
9 <expand macro="stdio" />
7
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 5
diff changeset
10 <expand macro="version_command" />
11
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
iuc
parents: 8
diff changeset
11 <command><![CDATA[
14
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
12
16
7c4ede6d88a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents: 14
diff changeset
13 snpEff databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g'
14
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
14
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
15 #if $include_pattern:
16
7c4ede6d88a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents: 14
diff changeset
16 | grep '${include_pattern}'
14
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
17 #end if
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
18
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
19 #if $exclude_pattern:
16
7c4ede6d88a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents: 14
diff changeset
20 | grep -v '${exclude_pattern}'
14
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
21 #end if
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
22
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
23 > '${snpeff_dbs}'
16
7c4ede6d88a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents: 14
diff changeset
24
11
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
iuc
parents: 8
diff changeset
25 ]]></command>
2
114f423f99c0 Uploaded
iuc
parents:
diff changeset
26 <inputs>
14
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
27 <param name="include_pattern" size="40" 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.">
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
28 <sanitizer>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
29 <valid initial="string.digits,string.letters">
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
30 <add value="^" />
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
31 </valid>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
32 </sanitizer>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
33 </param>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
34 <param name="exclude_pattern" size="40" 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.">
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
35 <sanitizer>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
36 <valid initial="string.digits,string.letters">
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
37 <add value="^" />
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
38 </valid>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
39 </sanitizer>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
40 </param>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
41
2
114f423f99c0 Uploaded
iuc
parents:
diff changeset
42 </inputs>
114f423f99c0 Uploaded
iuc
parents:
diff changeset
43 <outputs>
14
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
44 <data format="tabular" name="snpeff_dbs" label="${tool.name} @snpeff_version@ available databases" />
2
114f423f99c0 Uploaded
iuc
parents:
diff changeset
45 </outputs>
7
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 5
diff changeset
46 <tests>
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 5
diff changeset
47 <test>
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 5
diff changeset
48 <output name="snpeff_dbs">
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 5
diff changeset
49 <assert_contents>
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 5
diff changeset
50 <has_text text="ebola_zaire" />
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 5
diff changeset
51 </assert_contents>
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 5
diff changeset
52 </output>
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 5
diff changeset
53 </test>
14
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
54 <test>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
55 <param name="include_pattern" value="ebola"/>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
56 <output name="snpeff_dbs">
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
57 <assert_contents>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
58 <has_text text="ebola_zaire" />
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
59 </assert_contents>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
60 </output>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
61 </test>
7
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 5
diff changeset
62 </tests>
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 5
diff changeset
63 <help><![CDATA[
14
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
64
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
65 **What it does**
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
66
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
67 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::
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
68
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
69 mm10 Mouse http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_mm10.zip
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
70 mm9 Mouse http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_mm9.zip
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
71
16
7c4ede6d88a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents: 14
diff changeset
72 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).
14
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
73
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
74 -------
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
75
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
76 .. class:: infomark
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
77
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
78 **The usage scenario**
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
79
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
80 There are two ways to use names of databases obtained with this tool in Galaxy's version on snpEff:
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
81
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
82 #. 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.
16
7c4ede6d88a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents: 14
diff changeset
83 #. 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.
14
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
84
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
85 @snpeff_in_galaxy_info@
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 13
diff changeset
86 @external_documentation@
11
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
iuc
parents: 8
diff changeset
87 ]]></help>
7
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 5
diff changeset
88 <expand macro="citations" />
2
114f423f99c0 Uploaded
iuc
parents:
diff changeset
89 </tool>
114f423f99c0 Uploaded
iuc
parents:
diff changeset
90