Hi Jun and John,
we have a repository in the test toolshed that can address these use cases and much more ... I think ...
http://testtoolshed.g2.bx.psu.edu/view/bgruening/text_processing
Its based on the awesome unix-tools from Assaf Gordon and are mainly based on gnu core-utils with special patches for security concerns.
Development is happening here: https://github.com/bgruening/galaxytools/tree/master/text_processing
And I would appreciate any help :) @John haven’t looked at your wrappers, maybe they are worth to include?
Cheers, Bjoern
We have a pair of tools that do just this we (Jim Johnson and myself) have developed at MSI that have proven useful in a broad range of scenarios (these are implemented in Python instead of Perl). I have attached them if you are interested if using/extending them instead of building up new ones. I think there might be some other variations on this idea in the tool shed.
-John
On Fri, Oct 25, 2013 at 7:43 PM, Jun Fan j.fan@qmul.ac.uk wrote:
Hi all,
I am trying to develop a tool which allows the user to use regularexpression to only keep the lines matching the given pattern in the output. There are many special characters, e.g. \ in \d. In the perl script the wrapper invokes, the regular expression is printed as Xd+ for the regular expression \d+. My question is how to pass these special characters including , (, ), ^ etc. correctly into the perl script.
Best regards!
Jun
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/