Mercurial > repos > peterjc > blastxml_to_top_descr
diff tools/ncbi_blast_plus/blastxml_to_top_descr.xml @ 0:075fe5424c32 draft
Uploaded v0.0.1
author | peterjc |
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date | Thu, 07 Feb 2013 14:56:18 -0500 |
parents | |
children | 662fea0fe6b2 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.xml Thu Feb 07 14:56:18 2013 -0500 @@ -0,0 +1,47 @@ +<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.1"> + <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>