<tool id="blast2go" name="Blast2GO" version="0.0.1">
    <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. 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.

**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>