|
1
|
1 <tool id="blast2go" name="Blast2GO" version="0.0.2">
|
|
|
2 <description>Maps BLAST results to GO annotation terms</description>
|
|
|
3 <command interpreter="python">
|
|
|
4 blast2go.py $xml ${prop.fields.path} $tab
|
|
|
5 </command>
|
|
|
6 <inputs>
|
|
|
7 <param name="xml" type="data" format="blastxml" label="BLAST XML results" description="You must have run BLAST against a protein database such as the NCBI non-redundant (NR) database. Use BLASTX for nucleotide queries, BLASTP for protein queries." />
|
|
|
8 <param name="prop" type="select" label="Blast2GO settings" description="One or more configurations can be setup, such as using the Blast2GO team's server in Spain, or a local database.">
|
|
|
9 <options from_file="blast2go.loc">
|
|
|
10 <column name="value" index="0"/>
|
|
|
11 <column name="name" index="1"/>
|
|
|
12 <column name="path" index="2"/>
|
|
|
13 </options>
|
|
|
14 </param>
|
|
|
15 </inputs>
|
|
|
16 <outputs>
|
|
|
17 <data name="tab" format="tabular" label="Blast2GO ${prop.fields.name}" />
|
|
|
18 </outputs>
|
|
|
19 <requirements>
|
|
|
20 </requirements>
|
|
|
21 <tests>
|
|
|
22 </tests>
|
|
|
23 <help>
|
|
|
24 .. class:: warningmark
|
|
|
25
|
|
|
26 **Note**. Blast2GO may take a substantial amount of time, especially if
|
|
|
27 running against the public server in Spain. For large input datasets it
|
|
|
28 is advisable to allow overnight processing, or consider subdividing.
|
|
|
29
|
|
|
30 -----
|
|
|
31
|
|
|
32 **What it does**
|
|
|
33
|
|
|
34 This runs b2g4Pipe, the command line (no GUI) version of Blast2GO designed
|
|
|
35 for use in pipelines.
|
|
|
36
|
|
|
37 It takes as input BLAST XML results against a protein database, typically
|
|
|
38 the NCBI non-redundant (NR) database. This tool will accept concatenated
|
|
|
39 BLAST XML files (although they are technically invalid XML), which is very
|
|
|
40 useful if you have sub-divided your protein FASTA files and run BLAST on
|
|
|
41 them in batches.
|
|
|
42
|
|
|
43 The BLAST matches are used to assign Gene Ontology (GO) annotation terms
|
|
|
44 to each query sequence.
|
|
|
45
|
|
|
46 The output from this tool is a tabular file containing three columns, with
|
|
|
47 the order taken from query order in the original BLAST XML file:
|
|
|
48
|
|
|
49 ====== ====================================
|
|
|
50 Column Description
|
|
|
51 ------ ------------------------------------
|
|
|
52 1 ID and description of query sequence
|
|
|
53 2 GO term
|
|
|
54 3 GO description
|
|
|
55 ====== ====================================
|
|
|
56
|
|
|
57 Note that if no GO terms are assigned to a sequence (e.g. if it had no
|
|
|
58 BLAST matches), then it will not be present in the output file.
|
|
|
59
|
|
|
60
|
|
|
61 **Advanced Settings**
|
|
|
62
|
|
|
63 Blast2GO has a properties setting file which includes which database
|
|
|
64 server to connect to (e.g. the public server in Valencia, Spain, or a
|
|
|
65 local server), as well as more advanced options such as thresholds and
|
|
|
66 evidence code weights. To change these settings, your Galaxy administrator
|
|
|
67 must create a new properties file, and add it to the drop down menu above.
|
|
|
68
|
|
|
69
|
|
|
70 **References**
|
|
|
71
|
|
|
72 S. Götz et al.
|
|
|
73 High-throughput functional annotation and data mining with the Blast2GO suite.
|
|
|
74 Nucleic Acids Res. 36(10):3420–3435, 2008.
|
|
|
75 http://dx.doi.org/10.1093/nar/gkn176
|
|
|
76
|
|
|
77 A. Conesa and S. Götz.
|
|
|
78 Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
|
|
|
79 Int. J. Plant Genomics. 619832, 2008.
|
|
|
80 http://dx.doi.org/10.1155/2008/619832
|
|
|
81
|
|
|
82 A. Conesa et al.
|
|
|
83 Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
|
|
|
84 Bioinformatics 21:3674-3676, 2005.
|
|
|
85 http://dx.doi.org/10.1093/bioinformatics/bti610
|
|
|
86
|
|
|
87 http://www.blast2go.org/
|
|
|
88
|
|
|
89 </help>
|
|
|
90 </tool>
|
