annotate tools/blastxml_to_top_descr/blastxml_to_top_descr.xml @ 11:98f8431dab44 draft

Uploaded v0.1.0, now also handles extended tabular BLAST output.

<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.0">
    <description>Make a table from BLAST output</description>
    <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command>
    <command interpreter="python">
blastxml_to_top_descr.py
-f "$input.in_format"
#if $input.in_format == "tabular":
    --qseqid $input.qseqid
    --sseqid $input.sseqid
    --salltitles $input.salltitles
#end if
-o "${tabular_file}"
-t ${topN}
"${in_file}"
    </command>
    <stdio>
        <!-- Assume anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <inputs>
        <conditional name="input">
            <param name="in_format" type="select" label="Input format">
                <option value="blastxml" select="True">BLAST XML</option>
                <option value="tabular">Tabular</option>
            </param>
            <when value="blastxml">
                <param name="in_file" type="data" format="blastxml" label="BLAST results as XML"/>
            </when>
            <when value="tabular">
                <param name="in_file" type="data" format="tabular" label="BLAST results as tabular"/>
                <param name="qseqid" type="data_column" data_ref="in_file"
		       multiple="False" numerical="False" default_value="1" value="1"
		       label="Column containing query ID (qseqid)"
		       help="This is column 1 in standard BLAST tabular output" />
		<param name="sseqid" type="data_column" data_ref="in_file"
		       multiple="False" numerical="False" default_value="2" value="2"
		       label="Column containing match ID (sseqid)"
		       help="This is column 2 in standard BLAST tabular output"/>
                <param name="salltitles" type="data_column" data_ref="in_file"
		       multiple="False" numerical="False" default_value="25" value="25"
                       label="Column containing containing descriptions (salltitles)"
		       help="This is column 25 in the default extended BLAST tabular output"/>
            </when>
        </conditional>
        <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 $input.in_file.name" />
    </outputs>
    <requirements>
    </requirements>
    <tests>
        <test>
            <param name="in_format" value="blastxml" />
            <param name="in_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>
        <test>
            <param name="in_format" value="tabular" />
            <param name="in_file" value="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" />
            <param name="topN" value="3" />
            <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_top3_positive.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 until BLAST+ 2.2.28 the tabular output never included the
hit descriptions (titles) 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 (i.e. the first three). If
a query doesn't have that many hits, then these entries are left blank.

This tool can also be used with the tabular output from BLAST+ instead,
provided the relevant columns are provided. The default settings will
work with the default 25 column extended output from the BLAST+ tools
wrapped in Galaxy. Note if a query has *no* hits, it does not appear in
the BLAST tabular output.

**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>