Dear Galaxy team,
i would like to work on a few genomes that do not seem to be available on the system. Is it possible, and if yes how can i integrate those on Galaxy?
sincerely yours, Eric
Le 21 août 09 à 18:00, galaxy-user-request@bx.psu.edu a écrit :
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Today's Topics:
- Re: Passing a string with spaces to a tool (Nick Schurch)
- Re: Passing a string with spaces to a tool (James Casbon)
- Re: Passing a string with spaces to a tool (Gordon, Assaf)
- Problems with links in webpage output... (Nick Schurch)
- Re: Problems with links in webpage output... (Daniel Blankenberg)
Message: 1 Date: Fri, 21 Aug 2009 10:47:38 +0100 From: Nick Schurch N.Schurch@dundee.ac.uk Subject: Re: [galaxy-user] Passing a string with spaces to a tool To: galaxy-user@bx.psu.edu Message-ID: cb86364c0908210247m111c58cdv60ac45a1f8e7f775@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
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