Mercurial > repos > nilesh > tabix
comparison bgzip.xml @ 7:62ce37b4c6e1 draft default tip
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author | nilesh |
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date | Wed, 10 Jul 2013 17:20:54 -0400 |
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6:ea024cba4b7b | 7:62ce37b4c6e1 |
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1 <tool id="bgzip" name="bgzip" version="0.0.1"> | |
2 <description>Block compression/decompression utility. Required for use of tabix.</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.2.6">tabix</requirement> | |
5 </requirements> | |
6 <command> | |
7 bgzip | |
8 | |
9 #if str($virtualOffset) != "" | |
10 -b $virtualOffset | |
11 #end if | |
12 | |
13 #if str($size) != "" | |
14 -s $size | |
15 #end if | |
16 | |
17 $input | |
18 </command> | |
19 <inputs> | |
20 <param name="input" type="data" label="Input file" /> | |
21 <param name="virtualOffset" type="text" optional="yes" label="Virtual Offset" /> | |
22 <param name="size" type="text" optional="yes" label="Size" /> | |
23 </inputs> | |
24 | |
25 <outputs> | |
26 <data format= "bgz" name="output" from_work_dir="${input.file_name}.bgz"/> | |
27 </outputs> | |
28 | |
29 <help> | |
30 **What it does:** | |
31 | |
32 The input data file is sorted and compressed by bgzip which has a gzip(1) like interface. Tabix requires the file to be compressed using this tool first. | |
33 | |
34 **Citation:** | |
35 | |
36 Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching. | |
37 | |
38 http://samtools.sourceforge.net/tabix.shtml | |
39 | |
40 **Example:** | |
41 | |
42 (grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz; | |
43 | |
44 tabix -p gff sorted.gff.gz; | |
45 | |
46 tabix sorted.gff.gz chr1:10,000,000-20,000,000; | |
47 | |
48 </help> | |
49 </tool> |