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comparison tools/ncbi_blast_plus/blast2go.xml @ 1:0f159cf346c8

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Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 16:29:28 -0400
parents cd52c931b325
children e88a3246520e
comparison
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0:cd52c931b325 1:0f159cf346c8
1 <tool id="blast2go" name="Blast2GO" version="0.0.1"> 1 <tool id="blast2go" name="Blast2GO" version="0.0.2">
2 <description>Maps BLAST results to GO annotation terms</description> 2 <description>Maps BLAST results to GO annotation terms</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 blast2go.py $xml ${prop.fields.path} $tab 4 blast2go.py $xml ${prop.fields.path} $tab
5 </command> 5 </command>
6 <inputs> 6 <inputs>
33 33
34 This runs b2g4Pipe, the command line (no GUI) version of Blast2GO designed 34 This runs b2g4Pipe, the command line (no GUI) version of Blast2GO designed
35 for use in pipelines. 35 for use in pipelines.
36 36
37 It takes as input BLAST XML results against a protein database, typically 37 It takes as input BLAST XML results against a protein database, typically
38 the NCBI non-redundant (NR) database. The BLAST matches are used to assign 38 the NCBI non-redundant (NR) database. This tool will accept concatenated
39 Gene Ontology (GO) annotation terms to each query sequence. 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.
40 45
41 The output from this tool is a tabular file containing three columns, with 46 The output from this tool is a tabular file containing three columns, with
42 the order taken from query order in the original BLAST XML file: 47 the order taken from query order in the original BLAST XML file:
43 48
44 ====== ==================================== 49 ====== ====================================
49 3 GO description 54 3 GO description
50 ====== ==================================== 55 ====== ====================================
51 56
52 Note that if no GO terms are assigned to a sequence (e.g. if it had no 57 Note that if no GO terms are assigned to a sequence (e.g. if it had no
53 BLAST matches), then it will not be present in the output file. 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
54 69
55 **References** 70 **References**
56 71
57 S. Götz et al. 72 S. Götz et al.
58 High-throughput functional annotation and data mining with the Blast2GO suite. 73 High-throughput functional annotation and data mining with the Blast2GO suite.