# HG changeset patch
# User yating-l
# Date 1486073205 18000
# Node ID ad9a212044051db527db88bb79cbf5d2170ff217
# Parent  34c6f02de27f45563a6d9db09d941496b1322bbc
planemo upload commit 46cd27d5fb1b88220fb94b9039a685359b87d539

diff -r 34c6f02de27f -r ad9a21204405 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Feb 02 17:06:45 2017 -0500
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+Galaxy wrapper for UCSC pslCDnaFilter tool (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.
+
+parameters:
+-----------
+pslCDnaFilter parameters variable definitions by genome assembly category and type of cDNA sequence.
+
+# common paramters used for all assembly categories
+
+Same species: 
+  -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes
+
+Across species: 
+  -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes
+
+# common paramters used for local near best filtering
+
+Same species: 
+  -localNearBest=0.001 
+Across species: 
+  -localNearBest=0.010 
+
+# finished assemblies
+
+Same species: 
+  -minId=0.95 -minCover=0.25 
+Across species: 
+  -minId=0.35 -minCover=0.25 
+
+# well-ordered assemblies
+
+Same species: 
+  -minId=0.95 -minCover=0.15 
+Across species: 
+  -minId=0.35 -minCover=0.15 
+
+# low-coverage assemblies
+
+Same species: 
+  -minId=0.94 -minAlnSize=80 
+Across species: 
+  -minId=0.33 -minAlnSize=80 
+
+Reference:
+++++++++++
+`Configuration file for GenBank RefSeq alignment process <http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/hg/makeDb/genbank/etc/genbank.conf;h=03c4f3dcd12b48cf52feaf4d09561bf0a58ee352;hb=9447c3aa53839f2adbb3c2ef14ba8540a1dea077>`_
+
+
+Source code:
+-------------
+
+http://hgdownload.cse.ucsc.edu/admin/exe/
+
+Licence
+-------
+Please note that commercial download and installation of the Blat and In-Silico PCR software may be licensed through Kent Informatics (http://www.kentinformatics.com).