<tool id="blast2go" name="Blast2GO" version="0.0.2">
    <description>Maps BLAST results to GO annotation terms</description>
    <command interpreter="python">
        blast2go.py $xml ${prop.fields.path} $tab
    </command>
    <inputs>
        <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." /> 
        <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.">
             <options from_file="blast2go.loc">
                 <column name="value" index="0"/>
                 <column name="name" index="1"/>
                 <column name="path" index="2"/>
             </options>
        </param>
    </inputs>
    <outputs>
        <data name="tab" format="tabular" label="Blast2GO ${prop.fields.name}" />
    </outputs>
    <requirements>
    </requirements>
    <tests>
    </tests>
    <help>
.. class:: warningmark

**Note**. Blast2GO may take a substantial amount of time, especially if
running against the public server in Spain. For large input datasets it
is advisable to allow overnight processing, or consider subdividing.

-----

**What it does**

This runs b2g4Pipe, the command line (no GUI) version of Blast2GO designed
for use in pipelines.

It takes as input BLAST XML results against a protein database, typically
the NCBI non-redundant (NR) database. This tool will accept concatenated
BLAST XML files (although they are technically invalid XML), which is very
useful if you have sub-divided your protein FASTA files and run BLAST on
them in batches.

The BLAST matches are used to assign Gene Ontology (GO) annotation terms
to each query sequence.

The output from this tool is a tabular file containing three columns, with
the order taken from query order in the original BLAST XML file:

====== ====================================
Column Description
------ ------------------------------------
     1 ID and description of query sequence
     2 GO term
     3 GO description
====== ====================================

Note that if no GO terms are assigned to a sequence (e.g. if it had no
BLAST matches), then it will not be present in the output file.


**Advanced Settings**

Blast2GO has a properties setting file which includes which database
server to connect to (e.g. the public server in Valencia, Spain, or a
local server), as well as more advanced options such as thresholds and
evidence code weights. To change these settings, your Galaxy administrator
must create a new properties file, and add it to the drop down menu above.


**References**

S. Götz et al.
High-throughput functional annotation and data mining with the Blast2GO suite.
Nucleic Acids Res. 36(10):3420–3435, 2008.
http://dx.doi.org/10.1093/nar/gkn176

A. Conesa and S. Götz.
Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
Int. J. Plant Genomics. 619832, 2008.
http://dx.doi.org/10.1155/2008/619832

A. Conesa et al.
Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
Bioinformatics 21:3674-3676, 2005.
http://dx.doi.org/10.1093/bioinformatics/bti610

http://www.blast2go.org/

    </help>
</tool>