view blastxml_to_top_descr/blastxml_to_top_descr.xml @ 10:09a68a90d552 draft

Uploaded v0.0.9, updated citation information

<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.9">
    <description>Make a table from BLAST XML</description>
    <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command>
    <command interpreter="python">
      blastxml_to_top_descr.py "${blastxml_file}" "${tabular_file}" ${topN}
    </command>
    <stdio>
        <!-- Assume anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <inputs>
        <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> 
	<param name="topN" type="integer" min="1" max="100" optional="false" label="Number of descriptions" value="3"/>
    </inputs>
    <outputs>
        <data name="tabular_file" format="tabular" label="Top $topN descriptions from $blastxml_file.name" />
    </outputs>
    <requirements>
    </requirements>
    <tests>
        <test>
            <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
            <param name="topN" value="3" />
            <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_top3.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>

**What it does**

NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
formats including text, tabular and a more detailed XML format. You can
do a lot of things with tabular files in Galaxy (sorting, filtering, joins,
etc) however currently the BLAST tabular output omits the hit descriptions
found in the other output formats.

This tool turns a BLAST XML file into a simple tabular file containing
one row per query sequence, containing the query identifier and then
the three (by default) top hit descriptions. If a query doesn't have
that many hits, then these entries are left blank.

**Example Usage**

One simple usage would be to take a transcriptome assembly or set of
gene predictions, run a BLAST search against the NCBI NR database, and
then use this tool to make a table of the top three BLAST hits. This
can give you a 'quick and dirty' crude annotation, potentially enough
to spot some problems (e.g. bacterial contaimination could be very
obvious).

**References**

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

Peter J.A. Cock, Björn A. Grüning, 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

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

    </help>
</tool>