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 |
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date | Thu, 07 Feb 2013 14:56:18 -0500 |
parents | |
children | 662fea0fe6b2 |
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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> |