changeset 7:62ce37b4c6e1 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bgzip.xml	Wed Jul 10 17:20:54 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>
+        <requirement type="package" version="0.2.6">tabix</requirement>
+    </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>