Adding options to a tool

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Adding options to a tool

Scott Szakonyi
Hello all,

I am a new Galaxy admin/developer, so if this is as stupid question please be kind.

I am trying to add the ability for a user to choose additional parameters for Tophat for Illumina. After analyzing the Python and XML files in /galaxy-dist/tools/ngs_rna, I came to the conclusion that modifying these files would give me the desired results. However, no changes that I make to these files seem to have any effect whatsoever on the user experience inside the Galaxy server. I can not find any other likely candidates inside galaxy-dist. 

Am I looking in the wrong place? Is it even possible to add parameters to a tool interface?

Thanks in advance for any help you can offer.

--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556

http://crc.nd.edu


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Re: Adding options to a tool

Martin Čech
Hello Scott,

the tool named 'tophat' has been migrated out of distribution to the Tool Shed over a year ago. Which means that if it is in your Galaxy and your Galaxy is newer than a year it must have been installed from the Tool Shed. Tool Shed acts like an app store for Galaxy Tools. 

However the first thing I would check is whether the newer version of the tool (named tophat2) that we recently updated would suit your needs. You can try it on our Test instance here:
https://test.galaxyproject.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7

Please let me know if you have any questions and thank you for using Galaxy.

Martin, Galaxy Team

On Wed Feb 11 2015 at 4:36:08 PM Scott Szakonyi <[hidden email]> wrote:
Hello all,

I am a new Galaxy admin/developer, so if this is as stupid question please be kind.

I am trying to add the ability for a user to choose additional parameters for Tophat for Illumina. After analyzing the Python and XML files in /galaxy-dist/tools/ngs_rna, I came to the conclusion that modifying these files would give me the desired results. However, no changes that I make to these files seem to have any effect whatsoever on the user experience inside the Galaxy server. I can not find any other likely candidates inside galaxy-dist. 

Am I looking in the wrong place? Is it even possible to add parameters to a tool interface?

Thanks in advance for any help you can offer.

--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556

http://crc.nd.edu

___________________________________________________________
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Re: Adding options to a tool

Hans-Rudolf Hotz
Hi Scott

and just double checking, in case you do have an 'old' Galaxy installation:

after modifying the xml file  (I assume you are talking about
tophat_wrapper.xml?):  Have you re-loaded the tool?

click on 'Reload a tool's configuration' on the administration menu and
select the tool


Hans-Rudolf



Reload a tool's configuration
On 02/11/2015 11:00 PM, Martin Čech wrote:

> Hello Scott,
>
> the tool named 'tophat' has been migrated out of distribution to the
> Tool Shed over a year ago. Which means that if it is in your Galaxy and
> your Galaxy is newer than a year it must have been installed from the
> Tool Shed. Tool Shed acts like an app store for Galaxy Tools.
> The tophat tool is hosted here:
> https://toolshed.g2.bx.psu.edu/view/devteam/tophat
> and developed here:
> https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat
>
> However the first thing I would check is whether the newer version of
> the tool (named tophat2) that we recently updated would suit your needs.
> You can try it on our Test instance here:
> https://test.galaxyproject.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7
>
> Please let me know if you have any questions and thank you for using Galaxy.
>
> Martin, Galaxy Team
>
> On Wed Feb 11 2015 at 4:36:08 PM Scott Szakonyi
> <[hidden email] <mailto:[hidden email]>> wrote:
>
>     Hello all,
>
>     I am a new Galaxy admin/developer, so if this is as stupid question
>     please be kind.
>
>     I am trying to add the ability for a user to choose additional
>     parameters for Tophat for Illumina. After analyzing the Python and
>     XML files in /galaxy-dist/tools/ngs_rna, I came to the conclusion
>     that modifying these files would give me the desired results.
>     However, no changes that I make to these files seem to have any
>     effect whatsoever on the user experience inside the Galaxy server. I
>     can not find any other likely candidates inside galaxy-dist.
>
>     Am I looking in the wrong place? Is it even possible to add
>     parameters to a tool interface?
>
>     Thanks in advance for any help you can offer.
>
>     --
>     Scott B. Szakonyi
>     Research Programmer
>
>     *Center for Research Computing*
>     107 Information Technology Center
>     Notre Dame, IN 46556
>     http://crc.nd.edu <http://crc.nd.edu/>
>     _____________________________________________________________
>     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:
>     https://lists.galaxyproject.__org/ <https://lists.galaxyproject.org/>
>
>     To search Galaxy mailing lists use the unified search at:
>     http://galaxyproject.org/__search/mailinglists/
>     <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:
>    https://lists.galaxyproject.org/
>
> 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:
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