Hi all, A Cheetah question: when I enter ";" as a value in a text box of a tool (stored in $exp), Cheetah prints this as "X", and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
Hi Joachim, try that one: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_... Cheers, Bjoern
Hi all,
A Cheetah question: when I enter ";" as a value in a text box of a tool (stored in $exp), Cheetah prints this as "X", and passed this string to the tool.
How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail.
Thanks, Joachim
Thanks both of you! Okay, so I was looking in the wrong direction. This solved the issue. Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/24/2013 11:13 AM, Björn Grüning wrote:
Hi Joachim,
try that one: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_...
Cheers, Bjoern
Hi all,
A Cheetah question: when I enter ";" as a value in a text box of a tool (stored in $exp), Cheetah prints this as "X", and passed this string to the tool.
How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail.
Thanks, Joachim
On Wed, Jul 24, 2013 at 9:40 AM, Joachim Jacob | VIB | <joachim.jacob@vib.be> wrote:
Hi all,
A Cheetah question: when I enter ";" as a value in a text box of a tool (stored in $exp), Cheetah prints this as "X", and passed this string to the tool.
How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail.
Thanks, Joachim
That sounds like the Galaxy character sanitation making the change, things like pipes etc can have unexpected results in command lines. Have a look at the <sanitizer> tag for use in the tool's XML file. Peter
Okay, normally I would have forked the galaxy-dist and do a pull request with my change. But the change I want to commit is in the tool 'add_value', which is in the toolshed. Seems like a safer approach to me to contribute to the toolshed. How can I commit my changes to that tool? Can somebody of the devteam grant me acces? Do I send the diff by email :-) ? Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/24/2013 11:17 AM, Peter Cock wrote:
On Wed, Jul 24, 2013 at 9:40 AM, Joachim Jacob | VIB | <joachim.jacob@vib.be> wrote:
Hi all,
A Cheetah question: when I enter ";" as a value in a text box of a tool (stored in $exp), Cheetah prints this as "X", and passed this string to the tool.
How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail.
Thanks, Joachim That sounds like the Galaxy character sanitation making the change, things like pipes etc can have unexpected results in command lines. Have a look at the <sanitizer> tag for use in the tool's XML file.
Peter
Hi,
Okay, normally I would have forked the galaxy-dist and do a pull request with my change.
But the change I want to commit is in the tool 'add_value', which is in the toolshed. Seems like a safer approach to me to contribute to the toolshed. How can I commit my changes to that tool? Can somebody of the devteam grant me acces? Do I send the diff by email :-) ?
Yes, please send the patch to the mailing list and/or the devteam (toolshed should have a contact button). Also try to fill a trello card :) Thanks! Bjoern
Cheers, Joachim
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 07/24/2013 11:17 AM, Peter Cock wrote:
On Wed, Jul 24, 2013 at 9:40 AM, Joachim Jacob | VIB | <joachim.jacob@vib.be> wrote:
Hi all,
A Cheetah question: when I enter ";" as a value in a text box of a tool (stored in $exp), Cheetah prints this as "X", and passed this string to the tool.
How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail.
Thanks, Joachim That sounds like the Galaxy character sanitation making the change, things like pipes etc can have unexpected results in command lines. Have a look at the <sanitizer> tag for use in the tool's XML file.
Peter
On Wed, Jul 24, 2013 at 11:25 AM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Hi,
Okay, normally I would have forked the galaxy-dist and do a pull request with my change.
But the change I want to commit is in the tool 'add_value', which is in the toolshed. Seems like a safer approach to me to contribute to the toolshed. How can I commit my changes to that tool? Can somebody of the devteam grant me acces? Do I send the diff by email :-) ?
Yes, please send the patch to the mailing list and/or the devteam (toolshed should have a contact button). Also try to fill a trello card :)
Thanks! Bjoern
In general the upstream repository for a given tool will depend on the tool author's preferences. They may not even use a separate repository and work directly with the ToolShed in some cases. In other cases you might be able to contribute directly via a github pull request (planned for the NCBI BLAST+ tools), or a bitbucket pull request (the Galaxy team like bitbucket). The 'add_value' tool is under 'devteam' and it was original in the main Galaxy repository under BitBucket - I don't know where it lives now outside the tool shed: http://toolshed.g2.bx.psu.edu/view/devteam/add_value Regards, Peter
Hmm, seems that collaborating on tools is kind of a burden... Three places to notify this small change you say? (trello, galaxy-dev and direct emailing to the authors.) I have opted for Trello, card #1013 Cheers, J Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/24/2013 12:45 PM, Peter Cock wrote:
On Wed, Jul 24, 2013 at 11:25 AM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Hi,
Okay, normally I would have forked the galaxy-dist and do a pull request with my change.
But the change I want to commit is in the tool 'add_value', which is in the toolshed. Seems like a safer approach to me to contribute to the toolshed. How can I commit my changes to that tool? Can somebody of the devteam grant me acces? Do I send the diff by email :-) ? Yes, please send the patch to the mailing list and/or the devteam (toolshed should have a contact button). Also try to fill a trello card :)
Thanks! Bjoern In general the upstream repository for a given tool will depend on the tool author's preferences. They may not even use a separate repository and work directly with the ToolShed in some cases. In other cases you might be able to contribute directly via a github pull request (planned for the NCBI BLAST+ tools), or a bitbucket pull request (the Galaxy team like bitbucket).
The 'add_value' tool is under 'devteam' and it was original in the main Galaxy repository under BitBucket - I don't know where it lives now outside the tool shed: http://toolshed.g2.bx.psu.edu/view/devteam/add_value
Regards,
Peter
On Wed, Jul 24, 2013 at 1:56 PM, Joachim Jacob | VIB | <joachim.jacob@vib.be> wrote:
Hmm, seems that collaborating on tools is kind of a burden... Three places to notify this small change you say? (trello, galaxy-dev and direct emailing to the authors.)
I have opted for Trello, card #1013 Cheers,
https://trello.com/c/GVq8Vpsi/1013-bug-some-characters-not-permitted-in-add-... Well in this case the tool authors are the Galaxy Developers, so you can email them directly, via the galaxy-dev list, or their issue tracker which is Trello. Ideally every tool's README file would include contact details... Peter
participants (3)
-
Björn Grüning -
Joachim Jacob | VIB | -
Peter Cock