Add single quotes to the XML variable $str :

<command> mycommand.pl -str '$str' </command>

Then, spaces from the web interface will be preserved (single quoted, double quoted and other 'potentially unsafe' characters will still be converted into __sq__).

On Aug 21, 2009, at 5:48, "Nick Schurch" N.Schurch@dundee.ac.uk wrote:

Dear Galaxy-gurus,

How can I pass a string with spaces as a parameter from the galaxy interface to a tool that I've written myself in perl? I've tried enclosing the string with quotes (single and double) and various escape characters and all they do is add __dq/sq/X__ to the start of the string and then ignore everything else after the space.

my xml looks like:

<tool id="blah" name="mytool"> <command interpreter="perl"> /pathto/mycommand.pl -str $str </command> <inputs> <param name="str" type="text" label="Put your string here" />

The kind of commandline i'm looking for this to generate is....

perl mycommand.pl -str "this is my string"

but currently it just gives

perl mycommand.pl -str this or perl mycommand.pl -str __dq__this or perl mycommand.pl -str X__dq__this

Thanks!

-- Cheers,

Nick Schurch

Data Analysis Group (The Barton Group), School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK

Tel: +44 1382 388707 Fax: +44 1382 345 893 _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user