Tool Config Syntax Wiki page, <actions> tag

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Tool Config Syntax Wiki page, <actions> tag

Peter Cock
Hi,

There seems to be something wrong with the <actions> tag on the wiki page:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax

If doesn't appear in the table of contents, and there are three curly
brackets after the section name:
<actions>}}}

Peter
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Re: Tool Config Syntax Wiki page, <actions> tag

Fields, Christopher J
Is that from the wiki migration (differences in markup)?  I recall seeing this elsewhere on the galaxy wiki, seems to be slowly getting corrected.

chris

On Aug 4, 2011, at 10:30 AM, Peter Cock wrote:

> Hi,
>
> There seems to be something wrong with the <actions> tag on the wiki page:
> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
>
> If doesn't appear in the table of contents, and there are three curly
> brackets after the section name:
> <actions>}}}
>
> Peter
> ___________________________________________________________
> 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/


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Re: Tool Config Syntax Wiki page, <actions> tag

Jen Hillman-Jackson
In reply to this post by Peter Cock
Thanks Peter,

The wiki has been corrected, please let us know if you find anything
else in the current wiki. This was likely from the migration. The next
updated version of the public wiki is coming soon!

Best,

Jen
Galaxy team

On 8/4/11 8:30 AM, Peter Cock wrote:

> Hi,
>
> There seems to be something wrong with the<actions>  tag on the wiki page:
> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
>
> If doesn't appear in the table of contents, and there are three curly
> brackets after the section name:
> <actions>}}}
>
> Peter
> ___________________________________________________________
> 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/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
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Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: Tool Config Syntax Wiki page, <actions> tag

Peter Cock
On Fri, Aug 5, 2011 at 4:19 PM, Jennifer Jackson <[hidden email]> wrote:
> Thanks Peter,
>
> The wiki has been corrected, please let us know if you find anything else in
> the current wiki. This was likely from the migration. The next updated
> version of the public wiki is coming soon!
>
> Best,
>
> Jen

Thanks Jen,

I was hoping <actions> or something like that would allow a tool to
set column meta data on tabular output files. Is this possible?

Regards,

Peter
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Re: Tool Config Syntax Wiki page, <actions> tag

Daniel Blankenberg
Hi Peter,

Sorry for the delay in response.

The <outputs> <data> <actions> tagset will allow you to set metadata, including e.g. column assignments (start,end,strand,etc) for tabular (interval) files.  A somewhat complicated example of this is the cut tool (tools/filters/cutWrapper.xml), which sets output format to be interval (if required columns have been retained) and also sets the assigned columns to their new locations. Please let us know if this is not the information that you were interested it.

Thanks for using Galaxy,

Dan


On Aug 9, 2011, at 5:58 AM, Peter Cock wrote:

> On Fri, Aug 5, 2011 at 4:19 PM, Jennifer Jackson <[hidden email]> wrote:
>> Thanks Peter,
>>
>> The wiki has been corrected, please let us know if you find anything else in
>> the current wiki. This was likely from the migration. The next updated
>> version of the public wiki is coming soon!
>>
>> Best,
>>
>> Jen
>
> Thanks Jen,
>
> I was hoping <actions> or something like that would allow a tool to
> set column meta data on tabular output files. Is this possible?
>
> Regards,
>
> Peter
> ___________________________________________________________
> 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/


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