Hi Ross,

     Thank you very much for guiding me to use sanitize tag. I searched the forum and found this post extremely helpful http://gmod.827538.n3.nabble.com/preserving-newlines-in-input-parameters-td4022647.html. The problem got solved at least for now. One more question: is there anything like predefined set for all special characters, something like string.letters, string.digits ? Otherwise I have to define each of them in the add and remove list.

Best regards!

Jun

From: Ross [mailto:ross.lazarus@gmail.com]
Sent: 26 October 2013 03:07
To: Jun Fan
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] pass regular expression

Hi, Jun.

The inbuilt parameter sanitizer can be controlled - see http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set

The <valid> sub-tag allows precise control and you can specify eg string.printable if you want ANY printable character in your parameter

Here's an example from the Tool Factory:

 <param name="tool_name" type="text" value="My dynamic script"   label="New tool ID and title for outputs" size="60"

         help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with$

        <sanitizer invalid_char="">

            <valid initial="string.letters,string.digits"/>

        </sanitizer>

    </param>

I hope this helps?

On Sat, Oct 26, 2013 at 11:43 AM, 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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