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

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

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