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
Hi, Jun. The inbuilt parameter sanitizer can be controlled - see http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_... 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****
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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-td4.... 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_... 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<mailto: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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (4)
-
Björn Grüning -
John Chilton -
Jun Fan -
Ross