Mercurial > repos > peterjc > blast2go
comparison tools/ncbi_blast_plus/blast2go.xml @ 0:cd52c931b325
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
| author | peterjc |
|---|---|
| date | Tue, 07 Jun 2011 16:28:31 -0400 |
| parents | |
| children | 0f159cf346c8 |
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| -1:000000000000 | 0:cd52c931b325 |
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| 1 <tool id="blast2go" name="Blast2GO" version="0.0.1"> | |
| 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. The BLAST matches are used to assign | |
| 39 Gene Ontology (GO) annotation terms to each query sequence. | |
| 40 | |
| 41 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: | |
| 43 | |
| 44 ====== ==================================== | |
| 45 Column Description | |
| 46 ------ ------------------------------------ | |
| 47 1 ID and description of query sequence | |
| 48 2 GO term | |
| 49 3 GO description | |
| 50 ====== ==================================== | |
| 51 | |
| 52 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. | |
| 54 | |
| 55 **References** | |
| 56 | |
| 57 S. Götz et al. | |
| 58 High-throughput functional annotation and data mining with the Blast2GO suite. | |
| 59 Nucleic Acids Res. 36(10):3420–3435, 2008. | |
| 60 http://dx.doi.org/10.1093/nar/gkn176 | |
| 61 | |
| 62 A. Conesa and S. Götz. | |
| 63 Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics. | |
| 64 Int. J. Plant Genomics. 619832, 2008. | |
| 65 http://dx.doi.org/10.1155/2008/619832 | |
| 66 | |
| 67 A. Conesa et al. | |
| 68 Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. | |
| 69 Bioinformatics 21:3674-3676, 2005. | |
| 70 http://dx.doi.org/10.1093/bioinformatics/bti610 | |
| 71 | |
| 72 http://www.blast2go.org/ | |
| 73 | |
| 74 </help> | |
| 75 </tool> |