Mercurial > repos > peterjc > blastxml_to_top_descr
comparison tools/ncbi_blast_plus/blastxml_to_top_descr.xml @ 0:075fe5424c32 draft
Uploaded v0.0.1
| author | peterjc |
|---|---|
| date | Thu, 07 Feb 2013 14:56:18 -0500 |
| parents | |
| children | 662fea0fe6b2 |
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| -1:000000000000 | 0:075fe5424c32 |
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| 1 <tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.1"> | |
| 2 <description>Make a table from BLAST XML</description> | |
| 3 <command interpreter="python"> | |
| 4 blastxml_to_top_descr.py $blastxml_file $tabular_file $topN | |
| 5 </command> | |
| 6 <inputs> | |
| 7 <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> | |
| 8 <param name="topN" type="integer" min="1" max="100" optional="false" label="Number of descriptions" value="3"/> | |
| 9 </inputs> | |
| 10 <outputs> | |
| 11 <data name="tabular_file" format="tabular" label="Top $topN descriptions from $blastxml_file.name" /> | |
| 12 </outputs> | |
| 13 <requirements> | |
| 14 </requirements> | |
| 15 <tests> | |
| 16 <test> | |
| 17 <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> | |
| 18 <param name="topN" value="3" /> | |
| 19 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_top3.tabular" ftype="tabular" /> | |
| 20 </test> | |
| 21 </tests> | |
| 22 <help> | |
| 23 | |
| 24 **What it does** | |
| 25 | |
| 26 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of | |
| 27 formats including text, tabular and a more detailed XML format. You can | |
| 28 do a lot of things with tabular files in Galaxy (sorting, filtering, joins, | |
| 29 etc) however currently the BLAST tabular output omits the hit descriptions | |
| 30 found in the other output formats. | |
| 31 | |
| 32 This tool turns a BLAST XML file into a simple tabular file containing | |
| 33 one row per query sequence, containing the query identifier and then | |
| 34 the three (by default) top hit descriptions. If a query doesn't have | |
| 35 that many hits, then these entries are left blank. | |
| 36 | |
| 37 **Example Usage** | |
| 38 | |
| 39 One simple usage would be to take a transcriptome assembly or set of | |
| 40 gene predictions, run a BLAST search against the NCBI NR database, and | |
| 41 then use this tool to make a table of the top three BLAST hits. This | |
| 42 can give you a 'quick and dirty' crude annotation, potentially enough | |
| 43 to spot some problems (e.g. bacterial contaimination could be very | |
| 44 obvious). | |
| 45 | |
| 46 </help> | |
| 47 </tool> |