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....@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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