Mercurial > repos > xuebing > sharplabtool
comparison tools/filters/lav_to_bed.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 <tool id="lav_to_bed1" name="LAV to BED"> | |
2 <description>Converts a LAV formatted file to BED format</description> | |
3 <command interpreter="python">lav_to_bed.py $lav_file $bed_file1 $bed_file2</command> | |
4 <inputs> | |
5 <param name="lav_file" type="data" format="lav" label="LAV File" optional="False"/> | |
6 </inputs> | |
7 <outputs> | |
8 <data name="bed_file1" format="bed"/> | |
9 <data name="bed_file2" format="bed"/> | |
10 </outputs> | |
11 <tests> | |
12 <test> | |
13 <param name="lav_file" value="2.lav" ftype="lav" /> | |
14 <output name="bed_file2" file="lav_to_bed_out_1.bed" /> | |
15 <output name="bed_file2" file="lav_to_bed_out_2.bed" /> | |
16 </test> | |
17 </tests> | |
18 <help> | |
19 | |
20 **Syntax** | |
21 | |
22 This tool converts a LAV formatted file to the BED format. | |
23 | |
24 - **LAV format** LAV is an alignment format developed by Webb Miller's group at Penn State University. It is the primary output format for BLASTZ. | |
25 | |
26 - **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. | |
27 | |
28 ----- | |
29 | |
30 **Example** | |
31 | |
32 - Convert LAV format:: | |
33 | |
34 #:lav | |
35 s { | |
36 "/galaxy/data/hg16/seq/chr19.nib" 1 63811651 0 1 | |
37 "/galaxy/data/mm5/seq/chr11.nib" 1 121648857 0 1 | |
38 } | |
39 h { | |
40 "> hg16.chr19" | |
41 "> mm5.chr11 (reverse complement)" | |
42 } | |
43 a { | |
44 s 3500 | |
45 b 3001012 70568380 | |
46 e 3001075 70568443 | |
47 l 3001012 70568380 3001075 70568443 81 | |
48 } | |
49 a { | |
50 s 3900 | |
51 b 3008279 70573976 | |
52 e 3008357 70574054 | |
53 l 3008279 70573976 3008357 70574054 78 | |
54 } | |
55 #:eof | |
56 | |
57 - To two BED formatted files:: | |
58 | |
59 chr19 3001011 3001075 hg16_0 0 + | |
60 chr19 3008278 3008357 hg16_1 0 + | |
61 | |
62 **and**:: | |
63 | |
64 chr11 70568379 70568443 mm5_0 0 + | |
65 chr11 70573975 70574054 mm5_1 0 + | |
66 </help> | |
67 <code file="lav_to_bed_code.py"/> | |
68 </tool> |