annotate blast2go/blast2go.xml @ 6:872cf247c899 draft

Uploaded v0.0.8, auto-installation, RST README, MIT licence, citation information, development moved to GitHub, split out XML formatter into standalone script

<tool id="blast2go" name="Blast2GO" version="0.0.8">
    <description>Maps BLAST results to GO annotation terms</description>
    <requirements>
        <requirement type="package" version="2.5">b2g4pipe</requirement>
    </requirements>
    <command interpreter="python">
        blast2go.py "${xml}" "${prop.fields.path}" "${tab}"
    </command>
    <stdio>
        <!-- Wrapper ensures anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <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>
    <tests>
        <test>
            <param name="xml" value="blastp_sample.xml" ftype="blastxml"/>
            <param name="prop" value="Spain_2011_June"/>
            <output name="tab" file="blastp_sample.blast2go.tabular" ftype="tabular"/>
        </test>
    </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 v2.5, which is 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 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.

This tabular file is called an "Annotation File" in the Blast2GO GUI.
If you download the tabular file, and rename it to use the extension
".annot", then it can be opened with the Blast2GO GUI via the "File",
"Load Annotation (.annot)" menu (keyboard shortcut ALT+L). You can
then run some of the interactive analyses offered in the GUI tool.


**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**

If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers:

Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
Galaxy tools and workflows for sequence analysis with applications
in molecular plant pathology. PeerJ 1:e167
http://dx.doi.org/10.7717/peerj.167

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

A. Conesa and S. Götz (2008).
Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
International Journal of Plant Genomics. 619832.
http://dx.doi.org/10.1155/2008/619832

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

See also http://www.blast2go.com/

This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go

    </help>
</tool>