Mercurial > repos > iuc > snpeff

annotate snpEff_macros.xml @ 27:9473cd297a76 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 af2e922183065d2a950e07b4027cc6600503d38a
author iuc
date Wed, 22 Nov 2023 19:44:16 +0000
parents 5c7b70713fb5
children ca2b512e8d7c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
1 <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
2 <xml name="requirement">
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
3 <requirement type="package" version="4.3.1t">snpeff</requirement>
23
74aebe30fb52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 67da1a478db26ad45f36a673218d526f8962d72f"
iuc
parents: 17
diff changeset
4 <yield/>
0
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
5 </xml>
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
6 <xml name="stdio">
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
7 <stdio>
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
8 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
9 <exit_code range="1:" level="fatal" description="Error" />
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
10 </stdio>
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
11 </xml>
3
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
12 <xml name="version_command">
4
698ef30638a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
iuc
parents: 3
diff changeset
13 <version_command><![CDATA[
7
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
iuc
parents: 4
diff changeset
14 snpEff -version
4
698ef30638a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
iuc
parents: 3
diff changeset
15 ]]></version_command>
3
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
16 </xml>
17
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
iuc
parents: 15
diff changeset
17 <token name="@WRAPPER_VERSION@">4.3+T</token>
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
iuc
parents: 15
diff changeset
18 <token name="@SNPEFF_VERSION@">SnpEff4.3</token>
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
iuc
parents: 15
diff changeset
19 <token name="@SNPEFF_DATABASE_URL@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token>
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
iuc
parents: 15
diff changeset
20 <token name="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token>
25
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
21 <xml name="ref_select">
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
22 <conditional name="reference_source">
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
23 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
24 <option value="cached">Locally cached</option>
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
25 <option value="history">History</option>
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
26 </param>
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
27 <when value="cached">
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
28 <param name="ref_file" type="select" label="Select reference genome">
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
29 <options from_data_table="fasta_indexes"/>
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
30 </param>
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
31 </when>
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
32 <when value="history">
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
33 <param name="input_fasta" type="data" format="fasta,fasta.gz" label="Genome in FASTA format" help="This dataset is required for generating SnpEff database. See help section below."/>
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
34 </when>
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
35 </conditional>
5c7b70713fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3
iuc
parents: 24
diff changeset
36 </xml>
17
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
iuc
parents: 15
diff changeset
37 <token name="@EXTERNAL_DOCUMENTATION@">
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
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
39
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
40 -------
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
41
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
42 To learn more about snpEff read its manual at http://snpeff.sourceforge.net/SnpEff_manual.html
0
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
43 </token>
17
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
iuc
parents: 15
diff changeset
44 <token name="@SNPEFF_IN_GALAXY_INFO@">
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
45
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
46 -------
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
47
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
48 .. class:: warningmark
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
49
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
50 **Using SnpEff in Galaxy: A few points to remember**
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
51
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
52 SnpEff relies on specially formatted databases to generate annotations. It will not work without them. There are several ways in which these databases can be obtained.
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
53
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
54 **Pre-cached databases**
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
55
24
cfcf33df7fc0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4366b6a23223f84039a0590cf0d7079b83d8f84"
iuc
parents: 23
diff changeset
56 Many standard (e.g., human, mouse, *Drosophila*) databases are likely pre-cached within a given Galaxy instance. You should be able to see them listed in **Genome** drop-down of **SnpEff eff** tool.
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
57
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
58 In you *do not see them* keep reading...
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
59
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
60 **Download pre-built databases**
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
61
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
62 SnpEff project generates large numbers of pre-build databases. These are available at @SNPEFF_DATABASE_URL@ and can downloaded. Follow these steps:
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
63
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
64 #. Use **SnpEff databases** tool to generate a list of existing databases. Note the name of the database you need.
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
65 #. Use **SnpEff download** tool to download the database.
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
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.
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
67
12
5a29ab10dba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents: 10
diff changeset
68 Alternatively, you can specify the name of the database directly in **SnpEff eff** using the *Download on demand* option (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
69
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
70 **Create your own database**
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
71
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
72 In cases when you are dealing with bacterial or viral (or, frankly, any other) genomes it may be easier to create database yourself. For this you need:
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
73
15
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents: 12
diff changeset
74 #. Download Genbank record corresponding to your genome of interest from NCBI or use annotations in GFF format accompanied by the corresponding genome in FASTA format.
12
5a29ab10dba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents: 10
diff changeset
75 #. Use **SnpEff build** to create the database.
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
76 #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter).
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
77
15
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents: 12
diff changeset
78 Creating custom database has one major advantage. It guaranteess that you will not have any issues related to reference sequence naming -- the most common source of SnpEff errors.
10
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
79
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
80 </token>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
81
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
82
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents: 9
diff changeset
83
1
500832f27cbc Uploaded
iuc
parents: 0
diff changeset
84 <xml name="citations">
500832f27cbc Uploaded
iuc
parents: 0
diff changeset
85 <citations>
500832f27cbc Uploaded
iuc
parents: 0
diff changeset
86 <citation type="doi">10.4161/fly.19695</citation>
500832f27cbc Uploaded
iuc
parents: 0
diff changeset
87 <yield />
500832f27cbc Uploaded
iuc
parents: 0
diff changeset
88 </citations>
500832f27cbc Uploaded
iuc
parents: 0
diff changeset
89 </xml>
12
5a29ab10dba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents: 10
diff changeset
90 </macros>