Mercurial > repos > iuc > blastxml_to_gapped_gff3
comparison blastxml_to_gapped_gff3.xml @ 0:bd47051afe98 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
author | iuc |
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date | Tue, 20 Dec 2016 09:21:11 -0500 |
parents | |
children | 561e827baa5f |
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1 <tool id="blastxml_to_gapped_gff3" name="BlastXML to gapped GFF3" version="1.1"> | |
2 <description></description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <expand macro="stdio"/> | |
8 <version_command>python blastxml_to_gapped_gff3.py --version</version_command> | |
9 <command> | |
10 <![CDATA[ | |
11 python '$__tool_directory__/blastxml_to_gapped_gff3.py' | |
12 '$blastxml' | |
13 --min_gap $min_gap | |
14 $trim | |
15 > '$output' | |
16 ]]></command> | |
17 <inputs> | |
18 <param label="Blast XML" name="blastxml" type="data" format="blastxml"/> | |
19 <param label="Maximum gap size before generating a new match_part" name="min_gap" type="integer" value="3"/> | |
20 | |
21 <param type="select" label="Trim sides of blast hits" name="trim"> | |
22 <option value="">None</option> | |
23 <option value="--trim">Trim start and end</option> | |
24 <option value="--trim_end" selected="true">Trim only end</option> | |
25 </param> | |
26 </inputs> | |
27 <outputs> | |
28 <data format="gff3" name="output"/> | |
29 </outputs> | |
30 <tests> | |
31 <test> | |
32 <param name="blastxml" ftype="blastxml" value="input.xml"/> | |
33 <output name="output" file="blast.gff"/> | |
34 </test> | |
35 </tests> | |
36 <help><![CDATA[ | |
37 **What it does** | |
38 | |
39 Convert BlastXML results into GFF3 format. | |
40 | |
41 **Options** | |
42 | |
43 The trimming option captures an important feature provided in this tool that | |
44 isn't provided in most other BlastXML visualization tools: the fact that blast | |
45 captures complete alignment location information. | |
46 | |
47 This means that when most blast visualization tools produce output which looks | |
48 like this: | |
49 | |
50 .. image:: $PATH_TO_IMAGES/blast2html.png | |
51 | |
52 This tool produces output which shows where the real subject sequence starts and ends relative to your sequence: | |
53 | |
54 .. image:: $PATH_TO_IMAGES/blast-extended.png | |
55 | |
56 This can be a useful feature for examining alternate start locations that are | |
57 used by sequences found from your blast query. | |
58 | |
59 The green bars on the very top row of the picture indicate start sites, as you | |
60 can see the blast hits and the genome in the visualization share an upstream | |
61 start site. You don't lose the information present in your blastxml data. | |
62 | |
63 So, to the end of useful functionality, this options is controllable: | |
64 | |
65 - you can trim neither end, see where the real protein alignments are. | |
66 - you can trim both ends, like blasts HTML reports | |
67 - you can trim just the end of the sequence, as upstream is generally more | |
68 interesting, and having long tails can result in poor visualizations. | |
69 ]]></help> | |
70 <citations> | |
71 </citations> | |
72 </tool> | |
73 |