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author Lance Parsons <lparsons@princeton.edu>
date Mon, 16 May 2011 16:34:09 -0400
parents 8b064ea16722
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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