# HG changeset patch
# User yating-l
# Date 1485990197 18000
# Node ID bd3352c46beb9af164fb88bd9d1204cea71f647e
# Parent  6f06b6d68c0b00b31c9c4fdc948d16948d125510
planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty

diff -r 6f06b6d68c0b -r bd3352c46beb blat.xml
--- a/blat.xml	Wed Feb 01 17:52:37 2017 -0500
+++ b/blat.xml	Wed Feb 01 18:03:17 2017 -0500
@@ -124,31 +124,43 @@
 BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. 
 
 blat (version: v340)- Standalone blat sequence search command line tool. 
----------------------------------------------------------
+-------------------------------------------------------------------------
+
 usage:
 ++++++
-   blat database query [-ooc=11.ooc] output.psl
+
+  $ blat database query [-ooc=11.ooc] output.psl
+
 where:
    database and query are each either a .fa, .nib or .2bit file,
-      or a list of these files with one file name per line.
+   or a list of these files with one file name per line.
    -ooc=11.ooc tells the program to load over-occurring 11-mers from
-      an external file.  This will increase the speed
-      by a factor of 40 in many cases, but is not required.
-   output.psl is the name of the output file.   
+   an external file.  This will increase the speed
+   by a factor of 40 in many cases, but is not required.
+   output.psl is the name of the output file.  
+
 documentation:
 ++++++++++++++
-See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)  
+
+See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html) 
+
 Source code:
 ++++++++++++
+
 http://hgdownload.cse.ucsc.edu/admin/exe/
+
 pslCDnaFilter (version: v340)
----------------------------
+-----------------------------
 Filter cDNA alignments in psl format. Filtering criteria are comparative, selecting near best in genome alignments for each given cDNA and non-comparative, based only on the quality of an individual alignment.
+
 usage:
 ++++++
-      pslCDnaFilter [options] inPsl outPsl
+
+  $ pslCDnaFilter [options] inPsl outPsl
+
 Source code:
 ++++++++++++
+
 http://hgdownload.cse.ucsc.edu/admin/exe/
 
 Licence