Mercurial > repos > peterjc > blastxml_to_top_descr
view tools/blastxml_to_top_descr/blastxml_to_top_descr.xml @ 12:fe1ed74793c9 draft
Uploaded v0.1.1, embed citation in tool XML
author | peterjc |
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date | Wed, 30 Jul 2014 05:36:52 -0400 |
parents | 98f8431dab44 |
children | 8dc4ba7eba5d |
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<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.1"> <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> <citations> <citation type="doi">10.7717/peerj.167</citation> </citations> </tool>