Mercurial > repos > nilesh > tabix
changeset 6:ea024cba4b7b draft
Deleted selected files
| author | nilesh |
|---|---|
| date | Wed, 10 Jul 2013 17:20:39 -0400 |
| parents | 4be32b814be0 |
| children | 62ce37b4c6e1 |
| files | bgzip.xml |
| diffstat | 1 files changed, 0 insertions(+), 49 deletions(-) [+] |
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--- a/bgzip.xml Wed Jul 10 16:57:46 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ -<tool id="bgzip" name="bgzip" version="0.0.1"> - <description>Block compression/decompression utility. Required for use of tabix.</description> - <requirements> - <requirements type="package" version="0.2.6">tabix</requirements> - </requirements> - <command> - bgzip - - #if str($virtualOffset) != "" - -b $virtualOffset - #end if - - #if str($size) != "" - -s $size - #end if - - $input - </command> - <inputs> - <param name="input" type="data" label="Input file" /> - <param name="virtualOffset" type="text" optional="yes" label="Virtual Offset" /> - <param name="size" type="text" optional="yes" label="Size" /> - </inputs> - - <outputs> - <data format= "bgz" name="output" from_work_dir="${input.file_name}.bgz"/> - </outputs> - - <help> -**What it does:** - -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. - -**Citation:** - -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. - -http://samtools.sourceforge.net/tabix.shtml - -**Example:** - -(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz; - -tabix -p gff sorted.gff.gz; - -tabix sorted.gff.gz chr1:10,000,000-20,000,000; - - </help> -</tool>