Mercurial > repos > nilesh > tabix
changeset 5:4be32b814be0 draft
Uploaded
| author | nilesh |
|---|---|
| date | Wed, 10 Jul 2013 16:57:46 -0400 |
| parents | 148a92a4d0ed |
| children | ea024cba4b7b |
| files | bgzip.xml |
| diffstat | 1 files changed, 49 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bgzip.xml Wed Jul 10 16:57:46 2013 -0400 @@ -0,0 +1,49 @@ +<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>