Mercurial > repos > peterjc > blast2go
comparison tools/ncbi_blast_plus/blast2go.xml @ 1:0f159cf346c8
Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 16:29:28 -0400 |
parents | cd52c931b325 |
children | e88a3246520e |
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0:cd52c931b325 | 1:0f159cf346c8 |
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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. |