Mercurial > repos > peterjc > blastxml_to_top_descr
view tools/ncbi_blast_plus/blastxml_to_top_descr.xml @ 5:662fea0fe6b2 draft
Uploaded v0.0.4, quotes filenames in case the contain spaces
author | peterjc |
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date | Wed, 20 Feb 2013 13:36:37 -0500 |
parents | 075fe5424c32 |
children | 8a0771c5e236 |
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<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.4"> <description>Make a table from BLAST XML</description> <command interpreter="python"> blastxml_to_top_descr.py "${blastxml_file}" "${tabular_file}" ${topN} </command> <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). </help> </tool>