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Initial version with multiple adapter support
author Lance Parsons <lparsons@princeton.edu>
date Fri, 13 May 2011 15:54:01 -0400
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children 1dada50cca8a
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+++ b/README	Fri May 13 15:54:01 2011 -0400
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+Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/)
+
+Installation
+------------
+
+1 - Install the cutadapt package and make sure it is in path for Galaxy
+2 - Copy cutadapt.xml and cutadapt_galaxy_wrapper.py to $GALAXY_HOME/tools/cutadapt
+3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file
+
+
+Limitations
+-----------
+
+Colorspace data is not implemented
+Discard trimmed reads is not implemented (broken in cutadapt 0.9.3)
+Storing of "rest fo read" after the adapter (-r), too-short reads (--too-short-output), and untrimmed-reads (--untreimmed-output) are not implemented
+Quality cutoff (-q) not implemented
+Prefix and Suffix to read names not implemented
+Length-tag addition to read name not implemented