special character $ gets converted to X in tool

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special character $ gets converted to X in tool

Ketan Maheshwari
Hi,

In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying running script. However, it seems that the $ sign gets converted to X when it gets passed to the tool executable.

Is there a way to work around this or should I be doing something else to pass environment variables via Galaxy tool UI.

Thanks,
Ketan



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Re: special character $ gets converted to X in tool

Peter Cock
On Fri, Jan 31, 2014 at 5:13 PM, Ketan Maheshwari
<[hidden email]> wrote:

> Hi,
>
> In a test tool that I am working on, I need to enter text preceded by a $
> sign to be interpreted as an environment variable by the underlying running
> script. However, it seems that the $ sign gets converted to X when it gets
> passed to the tool executable.
>
> Is there a way to work around this or should I be doing something else to
> pass environment variables via Galaxy tool UI.
>
> Thanks,
> Ketan

This is a security feature I think - or it may just need escaping as \$

Since you are writing the script, why not pass in the environment
variable name without the dollar?

Peter
___________________________________________________________
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Re: special character $ gets converted to X in tool

Ketan Maheshwari
Thanks! 

Just wanted to report that \$ does not work; \ adds one more X.


On Fri, Jan 31, 2014 at 11:29 AM, Peter Cock <[hidden email]> wrote:
On Fri, Jan 31, 2014 at 5:13 PM, Ketan Maheshwari
<[hidden email]> wrote:
> Hi,
>
> In a test tool that I am working on, I need to enter text preceded by a $
> sign to be interpreted as an environment variable by the underlying running
> script. However, it seems that the $ sign gets converted to X when it gets
> passed to the tool executable.
>
> Is there a way to work around this or should I be doing something else to
> pass environment variables via Galaxy tool UI.
>
> Thanks,
> Ketan

This is a security feature I think - or it may just need escaping as \$

Since you are writing the script, why not pass in the environment
variable name without the dollar?

Peter



--
Ketan


___________________________________________________________
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Re: special character $ gets converted to X in tool

Björn Grüning-2
In reply to this post by Ketan Maheshwari
Hi Ketan!

it sounds like your input is sanitized. You can disable it for your
whole wrapper or you can write a special sanitizer for your input field:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set

Cheers,
Bjoern

> Hi,
>
>
> In a test tool that I am working on, I need to enter text preceded by
> a $ sign to be interpreted as an environment variable by the
> underlying running script. However, it seems that the $ sign gets
> converted to X when it gets passed to the tool executable.
>
>
> Is there a way to work around this or should I be doing something else
> to pass environment variables via Galaxy tool UI.
>
>
> Thanks,
> Ketan
>
>
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> 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/


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
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Re: special character $ gets converted to X in tool

Ketan Maheshwari
Thank you. It worked and the sanitizer tag sounds very useful.


On Sat, Feb 1, 2014 at 4:14 AM, Björn Grüning <[hidden email]> wrote:
Hi Ketan!

it sounds like your input is sanitized. You can disable it for your
whole wrapper or you can write a special sanitizer for your input field:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set

Cheers,
Bjoern

> Hi,
>
>
> In a test tool that I am working on, I need to enter text preceded by
> a $ sign to be interpreted as an environment variable by the
> underlying running script. However, it seems that the $ sign gets
> converted to X when it gets passed to the tool executable.
>
>
> Is there a way to work around this or should I be doing something else
> to pass environment variables via Galaxy tool UI.
>
>
> Thanks,
> Ketan
>
>
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> 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/





--
Ketan


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
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