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 regular expression 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
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