Tool Visibility

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Tool Visibility

Michael E. Cotterell
Suppose a tool didn't have any kind of configuration and therefore didn't need to be displayed in the "Analyze Data" part of Galaxy. Is there a way to modify tool_conf.xml so that a particular tool is only displayed in the Workflow editor?

Thanks!

Sincerely,
Michael E. Cotterell

Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA & TA, University of Georgia
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
http://michaelcotterell.com/


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Re: Tool Visibility

Michael E. Cotterell
Any ideas?

Thanks!

On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:

> Suppose a tool didn't have any kind of configuration and therefore didn't need to be displayed in the "Analyze Data" part of Galaxy. Is there a way to modify tool_conf.xml so that a particular tool is only displayed in the Workflow editor?
>
> Thanks!
>
> Sincerely,
> Michael E. Cotterell
>
> Ph.D. Student in Computer Science, University of Georgia
> Instructor of Record, Graduate RA & TA, University of Georgia
> [hidden email] (mailto:[hidden email])
> [hidden email] (mailto:[hidden email])
> [hidden email] (mailto:[hidden email])
> http://michaelcotterell.com/



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Re: Tool Visibility

Peter Cock
> On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:
>
>> Suppose a tool didn't have any kind of configuration and therefore didn't
>> need to be displayed in the "Analyze Data" part of Galaxy. Is there a way
>> to modify tool_conf.xml so that a particular tool is only displayed in the
>> Workflow editor?
>>
>> Thanks!
>>
>> Sincerely,
>> Michael E. Cotterell

On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
<[hidden email]> wrote:
> Any ideas?
>
> Thanks!

The only way this makes sense to me if is you have a tool with no inputs
at all (not even an input data file), but it produces one or more output files.
e.g. "Fetch the human genome as FASTA file, version hg18". But in that
case you'd be better off just defining the file within a shared data library.

Perhaps you could give an example of the kind of tool you are interested in?

Thanks,

Peter
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Re: Tool Visibility

Michael E. Cotterell
Peter,

Thanks for getting back to me.

I'm working on an existing project where my predecessors have added a tool that enables a user to add REST and SOAP Web services as usable tools within Galaxy by providing their WSDL or WADL URLs. It makes sense that the tools that are added should show up in both the "Analyze" page and the Workflow editor, but the actual tool for adding Web services is not intended to be used in workflows.

I understand that this tool should probably (more appropriately) be located on the "Admin" page, but in the short run, I'd like to hide this tool from showing up in the list of tools available in the Workflow editor (admittedly, this is the opposite of my original question).
In the long run, is there an API for adding plugins (or similar) to the admin page? I ask because this particular tool is not designed to be used in a workflow, but rather, it is designed to add tools to Galaxy itself.

Perhaps there is a way to work this into the Toolshed stuff you guys are working on?

Any thoughts are much appreciated.

Thanks!

Sincerely,
Michael E. Cotterell

Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA & TA, University of Georgia
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
http://michaelcotterell.com/


On Wednesday, June 5, 2013 at 11:08 AM, Peter Cock wrote:

> > On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:
> >
> > > Suppose a tool didn't have any kind of configuration and therefore didn't
> > > need to be displayed in the "Analyze Data" part of Galaxy. Is there a way
> > > to modify tool_conf.xml so that a particular tool is only displayed in the
> > > Workflow editor?
> > >
> > > Thanks!
> > >
> > > Sincerely,
> > > Michael E. Cotterell
> >
>
>
>
> On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
> <[hidden email] (mailto:[hidden email])> wrote:
> > Any ideas?
> >
> > Thanks!
>
> The only way this makes sense to me if is you have a tool with no inputs
> at all (not even an input data file), but it produces one or more output files.
> e.g. "Fetch the human genome as FASTA file, version hg18". But in that
> case you'd be better off just defining the file within a shared data library.
>
> Perhaps you could give an example of the kind of tool you are interested in?
>
> Thanks,
>
> Peter


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Re: Tool Visibility

John Chilton
Add workflow_ compatible ="false" to the tool XML element to hide it
in the workflow editor. Check the tools/data_source/upload.xml for an
example of this.

If you would like to hide it both in the workflow editor and the side
bar but still allow for other direct links to it you can setup dynamic
toolbox filters (you will need to manually pull in the pull request
changes as this has not been merged by the Galaxy team):

https://bitbucket.org/galaxy/galaxy-central/pull-request/160/implement-dynamic-toolbox-filters

These can even let you show it to your admins in their side panel, but
not to other users. This way you don't have to hack up the admin
section of the UI.

Additionally, you may want to go one step further and prevent others
from using the tool (not just preventing them from seeing it). To do
this, you can use dynamic job destinations and prevent these tools
from running for non-admins:

http://wiki.galaxyproject.org/Admin/Config/Jobs

-John


On Wed, Jun 5, 2013 at 10:37 AM, Michael E. Cotterell
<[hidden email]> wrote:

> Peter,
>
> Thanks for getting back to me.
>
> I'm working on an existing project where my predecessors have added a tool that enables a user to add REST and SOAP Web services as usable tools within Galaxy by providing their WSDL or WADL URLs. It makes sense that the tools that are added should show up in both the "Analyze" page and the Workflow editor, but the actual tool for adding Web services is not intended to be used in workflows.
>
> I understand that this tool should probably (more appropriately) be located on the "Admin" page, but in the short run, I'd like to hide this tool from showing up in the list of tools available in the Workflow editor (admittedly, this is the opposite of my original question).
> In the long run, is there an API for adding plugins (or similar) to the admin page? I ask because this particular tool is not designed to be used in a workflow, but rather, it is designed to add tools to Galaxy itself.
>
> Perhaps there is a way to work this into the Toolshed stuff you guys are working on?
>
> Any thoughts are much appreciated.
>
> Thanks!
>
> Sincerely,
> Michael E. Cotterell
>
> Ph.D. Student in Computer Science, University of Georgia
> Instructor of Record, Graduate RA & TA, University of Georgia
> [hidden email] (mailto:[hidden email])
> [hidden email] (mailto:[hidden email])
> [hidden email] (mailto:[hidden email])
> http://michaelcotterell.com/
>
>
> On Wednesday, June 5, 2013 at 11:08 AM, Peter Cock wrote:
>
>> > On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:
>> >
>> > > Suppose a tool didn't have any kind of configuration and therefore didn't
>> > > need to be displayed in the "Analyze Data" part of Galaxy. Is there a way
>> > > to modify tool_conf.xml so that a particular tool is only displayed in the
>> > > Workflow editor?
>> > >
>> > > Thanks!
>> > >
>> > > Sincerely,
>> > > Michael E. Cotterell
>> >
>>
>>
>>
>> On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
>> <[hidden email] (mailto:[hidden email])> wrote:
>> > Any ideas?
>> >
>> > Thanks!
>>
>> The only way this makes sense to me if is you have a tool with no inputs
>> at all (not even an input data file), but it produces one or more output files.
>> e.g. "Fetch the human genome as FASTA file, version hg18". But in that
>> case you'd be better off just defining the file within a shared data library.
>>
>> Perhaps you could give an example of the kind of tool you are interested in?
>>
>> Thanks,
>>
>> 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/
>
> 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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Re: Tool Visibility

Michael E. Cotterell
This is great! Will it work with sections as well?

Thanks!

Sincerely,
Michael E. Cotterell

Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA & TA, University of Georgia
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
http://michaelcotterell.com/


On Wednesday, June 5, 2013 at 11:49 AM, John Chilton wrote:

> Add workflow_ compatible ="false" to the tool XML element to hide it
> in the workflow editor. Check the tools/data_source/upload.xml for an
> example of this.
>
> If you would like to hide it both in the workflow editor and the side
> bar but still allow for other direct links to it you can setup dynamic
> toolbox filters (you will need to manually pull in the pull request
> changes as this has not been merged by the Galaxy team):
>
> https://bitbucket.org/galaxy/galaxy-central/pull-request/160/implement-dynamic-toolbox-filters
>
> These can even let you show it to your admins in their side panel, but
> not to other users. This way you don't have to hack up the admin
> section of the UI.
>
> Additionally, you may want to go one step further and prevent others
> from using the tool (not just preventing them from seeing it). To do
> this, you can use dynamic job destinations and prevent these tools
> from running for non-admins:
>
> http://wiki.galaxyproject.org/Admin/Config/Jobs
>
> -John
>
>
> On Wed, Jun 5, 2013 at 10:37 AM, Michael E. Cotterell
> <[hidden email] (mailto:[hidden email])> wrote:
> > Peter,
> >
> > Thanks for getting back to me.
> >
> > I'm working on an existing project where my predecessors have added a tool that enables a user to add REST and SOAP Web services as usable tools within Galaxy by providing their WSDL or WADL URLs. It makes sense that the tools that are added should show up in both the "Analyze" page and the Workflow editor, but the actual tool for adding Web services is not intended to be used in workflows.
> >
> > I understand that this tool should probably (more appropriately) be located on the "Admin" page, but in the short run, I'd like to hide this tool from showing up in the list of tools available in the Workflow editor (admittedly, this is the opposite of my original question).
> > In the long run, is there an API for adding plugins (or similar) to the admin page? I ask because this particular tool is not designed to be used in a workflow, but rather, it is designed to add tools to Galaxy itself.
> >
> > Perhaps there is a way to work this into the Toolshed stuff you guys are working on?
> >
> > Any thoughts are much appreciated.
> >
> > Thanks!
> >
> > Sincerely,
> > Michael E. Cotterell
> >
> > Ph.D. Student in Computer Science, University of Georgia
> > Instructor of Record, Graduate RA & TA, University of Georgia
> > [hidden email] (mailto:[hidden email])
> > [hidden email] (mailto:[hidden email])
> > [hidden email] (mailto:[hidden email])
> > http://michaelcotterell.com/
> >
> >
> > On Wednesday, June 5, 2013 at 11:08 AM, Peter Cock wrote:
> >
> > > > On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:
> > > >
> > > > > Suppose a tool didn't have any kind of configuration and therefore didn't
> > > > > need to be displayed in the "Analyze Data" part of Galaxy. Is there a way
> > > > > to modify tool_conf.xml so that a particular tool is only displayed in the
> > > > > Workflow editor?
> > > > >
> > > > > Thanks!
> > > > >
> > > > > Sincerely,
> > > > > Michael E. Cotterell
> > > >
> > >
> > >
> > >
> > >
> > >
> > > On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
> > > <[hidden email] (mailto:[hidden email])> wrote:
> > > > Any ideas?
> > > >
> > > > Thanks!
> > >
> > > The only way this makes sense to me if is you have a tool with no inputs
> > > at all (not even an input data file), but it produces one or more output files.
> > > e.g. "Fetch the human genome as FASTA file, version hg18". But in that
> > > case you'd be better off just defining the file within a shared data library.
> > >
> > > Perhaps you could give an example of the kind of tool you are interested in?
> > >
> > > Thanks,
> > >
> > > 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/
> >
> > 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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Re: Tool Visibility

Peter Cock
In reply to this post by Michael E. Cotterell
On Wed, Jun 5, 2013 at 4:37 PM, Michael E. Cotterell
<[hidden email]> wrote:

> Peter,
>
> Thanks for getting back to me.
>
> I'm working on an existing project where my predecessors have added a tool that enables a user to add REST and SOAP Web services as usable tools within Galaxy by providing their WSDL or WADL URLs. It makes sense that the tools that are added should show up in both the "Analyze" page and the Workflow editor, but the actual tool for adding Web services is not intended to be used in workflows.
>
> I understand that this tool should probably (more appropriately) be located on the "Admin" page, but in the short run, I'd like to hide this tool from showing up in the list of tools available in the Workflow editor (admittedly, this is the opposite of my original question).
> In the long run, is there an API for adding plugins (or similar) to the admin page? I ask because this particular tool is not designed to be used in a workflow, but rather, it is designed to add tools to Galaxy itself.
>
> Perhaps there is a way to work this into the Toolshed stuff you guys are working on?
>
> Any thoughts are much appreciated.
>
> Thanks!
>
> Sincerely,
> Michael E. Cotterell

I can see similarities to the part of the "Tool Shed Factory" program,
http://www.ncbi.nlm.nih.gov/pubmed/23024011

Peter

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Re: Tool Visibility

John Chilton
In reply to this post by Michael E. Cotterell
Yes to the toolbox filters, no the dynamic job destinations (these
need to be configured per tool).

Look at the last example included with the pull request -
per_host_tool_sections for an example of how to configure tool section
filters.

-John


On Wed, Jun 5, 2013 at 10:51 AM, Michael E. Cotterell
<[hidden email]> wrote:

> This is great! Will it work with sections as well?
>
> Thanks!
>
> Sincerely,
> Michael E. Cotterell
>
> Ph.D. Student in Computer Science, University of Georgia
> Instructor of Record, Graduate RA & TA, University of Georgia
> [hidden email] (mailto:[hidden email])
> [hidden email] (mailto:[hidden email])
> [hidden email] (mailto:[hidden email])
> http://michaelcotterell.com/
>
>
> On Wednesday, June 5, 2013 at 11:49 AM, John Chilton wrote:
>
>> Add workflow_ compatible ="false" to the tool XML element to hide it
>> in the workflow editor. Check the tools/data_source/upload.xml for an
>> example of this.
>>
>> If you would like to hide it both in the workflow editor and the side
>> bar but still allow for other direct links to it you can setup dynamic
>> toolbox filters (you will need to manually pull in the pull request
>> changes as this has not been merged by the Galaxy team):
>>
>> https://bitbucket.org/galaxy/galaxy-central/pull-request/160/implement-dynamic-toolbox-filters
>>
>> These can even let you show it to your admins in their side panel, but
>> not to other users. This way you don't have to hack up the admin
>> section of the UI.
>>
>> Additionally, you may want to go one step further and prevent others
>> from using the tool (not just preventing them from seeing it). To do
>> this, you can use dynamic job destinations and prevent these tools
>> from running for non-admins:
>>
>> http://wiki.galaxyproject.org/Admin/Config/Jobs
>>
>> -John
>>
>>
>> On Wed, Jun 5, 2013 at 10:37 AM, Michael E. Cotterell
>> <[hidden email] (mailto:[hidden email])> wrote:
>> > Peter,
>> >
>> > Thanks for getting back to me.
>> >
>> > I'm working on an existing project where my predecessors have added a tool that enables a user to add REST and SOAP Web services as usable tools within Galaxy by providing their WSDL or WADL URLs. It makes sense that the tools that are added should show up in both the "Analyze" page and the Workflow editor, but the actual tool for adding Web services is not intended to be used in workflows.
>> >
>> > I understand that this tool should probably (more appropriately) be located on the "Admin" page, but in the short run, I'd like to hide this tool from showing up in the list of tools available in the Workflow editor (admittedly, this is the opposite of my original question).
>> > In the long run, is there an API for adding plugins (or similar) to the admin page? I ask because this particular tool is not designed to be used in a workflow, but rather, it is designed to add tools to Galaxy itself.
>> >
>> > Perhaps there is a way to work this into the Toolshed stuff you guys are working on?
>> >
>> > Any thoughts are much appreciated.
>> >
>> > Thanks!
>> >
>> > Sincerely,
>> > Michael E. Cotterell
>> >
>> > Ph.D. Student in Computer Science, University of Georgia
>> > Instructor of Record, Graduate RA & TA, University of Georgia
>> > [hidden email] (mailto:[hidden email])
>> > [hidden email] (mailto:[hidden email])
>> > [hidden email] (mailto:[hidden email])
>> > http://michaelcotterell.com/
>> >
>> >
>> > On Wednesday, June 5, 2013 at 11:08 AM, Peter Cock wrote:
>> >
>> > > > On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:
>> > > >
>> > > > > Suppose a tool didn't have any kind of configuration and therefore didn't
>> > > > > need to be displayed in the "Analyze Data" part of Galaxy. Is there a way
>> > > > > to modify tool_conf.xml so that a particular tool is only displayed in the
>> > > > > Workflow editor?
>> > > > >
>> > > > > Thanks!
>> > > > >
>> > > > > Sincerely,
>> > > > > Michael E. Cotterell
>> > > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
>> > > <[hidden email] (mailto:[hidden email])> wrote:
>> > > > Any ideas?
>> > > >
>> > > > Thanks!
>> > >
>> > > The only way this makes sense to me if is you have a tool with no inputs
>> > > at all (not even an input data file), but it produces one or more output files.
>> > > e.g. "Fetch the human genome as FASTA file, version hg18". But in that
>> > > case you'd be better off just defining the file within a shared data library.
>> > >
>> > > Perhaps you could give an example of the kind of tool you are interested in?
>> > >
>> > > Thanks,
>> > >
>> > > 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/
>> >
>> > 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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Re: Tool Visibility

Michael E. Cotterell
In reply to this post by John Chilton
John,

Is there a way to hide an entire section (not just make it greyed out) using the most recent galaxy-dist?

I'm investigating the pull request you linked to, and it looks interesting, but is it compatible with galaxy-dist (it's on the bitbucket page for galaxy-central)?

Thanks!

Sincerely,
Michael E. Cotterell

Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA & TA, University of Georgia
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
http://michaelcotterell.com/


On Wednesday, June 5, 2013 at 11:49 AM, John Chilton wrote:

> Add workflow_ compatible ="false" to the tool XML element to hide it
> in the workflow editor. Check the tools/data_source/upload.xml for an
> example of this.
>
> If you would like to hide it both in the workflow editor and the side
> bar but still allow for other direct links to it you can setup dynamic
> toolbox filters (you will need to manually pull in the pull request
> changes as this has not been merged by the Galaxy team):
>
> https://bitbucket.org/galaxy/galaxy-central/pull-request/160/implement-dynamic-toolbox-filters
>
> These can even let you show it to your admins in their side panel, but
> not to other users. This way you don't have to hack up the admin
> section of the UI.
>
> Additionally, you may want to go one step further and prevent others
> from using the tool (not just preventing them from seeing it). To do
> this, you can use dynamic job destinations and prevent these tools
> from running for non-admins:
>
> http://wiki.galaxyproject.org/Admin/Config/Jobs
>
> -John
>
>
> On Wed, Jun 5, 2013 at 10:37 AM, Michael E. Cotterell
> <[hidden email] (mailto:[hidden email])> wrote:
> > Peter,
> >
> > Thanks for getting back to me.
> >
> > I'm working on an existing project where my predecessors have added a tool that enables a user to add REST and SOAP Web services as usable tools within Galaxy by providing their WSDL or WADL URLs. It makes sense that the tools that are added should show up in both the "Analyze" page and the Workflow editor, but the actual tool for adding Web services is not intended to be used in workflows.
> >
> > I understand that this tool should probably (more appropriately) be located on the "Admin" page, but in the short run, I'd like to hide this tool from showing up in the list of tools available in the Workflow editor (admittedly, this is the opposite of my original question).
> > In the long run, is there an API for adding plugins (or similar) to the admin page? I ask because this particular tool is not designed to be used in a workflow, but rather, it is designed to add tools to Galaxy itself.
> >
> > Perhaps there is a way to work this into the Toolshed stuff you guys are working on?
> >
> > Any thoughts are much appreciated.
> >
> > Thanks!
> >
> > Sincerely,
> > Michael E. Cotterell
> >
> > Ph.D. Student in Computer Science, University of Georgia
> > Instructor of Record, Graduate RA & TA, University of Georgia
> > [hidden email] (mailto:[hidden email])
> > [hidden email] (mailto:[hidden email])
> > [hidden email] (mailto:[hidden email])
> > http://michaelcotterell.com/
> >
> >
> > On Wednesday, June 5, 2013 at 11:08 AM, Peter Cock wrote:
> >
> > > > On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:
> > > >
> > > > > Suppose a tool didn't have any kind of configuration and therefore didn't
> > > > > need to be displayed in the "Analyze Data" part of Galaxy. Is there a way
> > > > > to modify tool_conf.xml so that a particular tool is only displayed in the
> > > > > Workflow editor?
> > > > >
> > > > > Thanks!
> > > > >
> > > > > Sincerely,
> > > > > Michael E. Cotterell
> > > >
> > >
> > >
> > >
> > >
> > >
> > > On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
> > > <[hidden email] (mailto:[hidden email])> wrote:
> > > > Any ideas?
> > > >
> > > > Thanks!
> > >
> > > The only way this makes sense to me if is you have a tool with no inputs
> > > at all (not even an input data file), but it produces one or more output files.
> > > e.g. "Fetch the human genome as FASTA file, version hg18". But in that
> > > case you'd be better off just defining the file within a shared data library.
> > >
> > > Perhaps you could give an example of the kind of tool you are interested in?
> > >
> > > Thanks,
> > >
> > > 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/
> >
> > To search Galaxy mailing lists use the unified search at:
> > http://galaxyproject.org/search/mailinglists/
>



___________________________________________________________
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Re: Tool Visibility

John Chilton
If you look at the date on the pull request it looks like it was a
full month before they even froze central for the last dist release,
so at this point I would be more confident it is going to work with
galaxy-dist than galaxy-central.

-John

On Wed, Jun 5, 2013 at 11:04 AM, Michael E. Cotterell
<[hidden email]> wrote:

> John,
>
> Is there a way to hide an entire section (not just make it greyed out) using the most recent galaxy-dist?
>
> I'm investigating the pull request you linked to, and it looks interesting, but is it compatible with galaxy-dist (it's on the bitbucket page for galaxy-central)?
>
> Thanks!
>
> Sincerely,
> Michael E. Cotterell
>
> Ph.D. Student in Computer Science, University of Georgia
> Instructor of Record, Graduate RA & TA, University of Georgia
> [hidden email] (mailto:[hidden email])
> [hidden email] (mailto:[hidden email])
> [hidden email] (mailto:[hidden email])
> http://michaelcotterell.com/
>
>
> On Wednesday, June 5, 2013 at 11:49 AM, John Chilton wrote:
>
>> Add workflow_ compatible ="false" to the tool XML element to hide it
>> in the workflow editor. Check the tools/data_source/upload.xml for an
>> example of this.
>>
>> If you would like to hide it both in the workflow editor and the side
>> bar but still allow for other direct links to it you can setup dynamic
>> toolbox filters (you will need to manually pull in the pull request
>> changes as this has not been merged by the Galaxy team):
>>
>> https://bitbucket.org/galaxy/galaxy-central/pull-request/160/implement-dynamic-toolbox-filters
>>
>> These can even let you show it to your admins in their side panel, but
>> not to other users. This way you don't have to hack up the admin
>> section of the UI.
>>
>> Additionally, you may want to go one step further and prevent others
>> from using the tool (not just preventing them from seeing it). To do
>> this, you can use dynamic job destinations and prevent these tools
>> from running for non-admins:
>>
>> http://wiki.galaxyproject.org/Admin/Config/Jobs
>>
>> -John
>>
>>
>> On Wed, Jun 5, 2013 at 10:37 AM, Michael E. Cotterell
>> <[hidden email] (mailto:[hidden email])> wrote:
>> > Peter,
>> >
>> > Thanks for getting back to me.
>> >
>> > I'm working on an existing project where my predecessors have added a tool that enables a user to add REST and SOAP Web services as usable tools within Galaxy by providing their WSDL or WADL URLs. It makes sense that the tools that are added should show up in both the "Analyze" page and the Workflow editor, but the actual tool for adding Web services is not intended to be used in workflows.
>> >
>> > I understand that this tool should probably (more appropriately) be located on the "Admin" page, but in the short run, I'd like to hide this tool from showing up in the list of tools available in the Workflow editor (admittedly, this is the opposite of my original question).
>> > In the long run, is there an API for adding plugins (or similar) to the admin page? I ask because this particular tool is not designed to be used in a workflow, but rather, it is designed to add tools to Galaxy itself.
>> >
>> > Perhaps there is a way to work this into the Toolshed stuff you guys are working on?
>> >
>> > Any thoughts are much appreciated.
>> >
>> > Thanks!
>> >
>> > Sincerely,
>> > Michael E. Cotterell
>> >
>> > Ph.D. Student in Computer Science, University of Georgia
>> > Instructor of Record, Graduate RA & TA, University of Georgia
>> > [hidden email] (mailto:[hidden email])
>> > [hidden email] (mailto:[hidden email])
>> > [hidden email] (mailto:[hidden email])
>> > http://michaelcotterell.com/
>> >
>> >
>> > On Wednesday, June 5, 2013 at 11:08 AM, Peter Cock wrote:
>> >
>> > > > On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:
>> > > >
>> > > > > Suppose a tool didn't have any kind of configuration and therefore didn't
>> > > > > need to be displayed in the "Analyze Data" part of Galaxy. Is there a way
>> > > > > to modify tool_conf.xml so that a particular tool is only displayed in the
>> > > > > Workflow editor?
>> > > > >
>> > > > > Thanks!
>> > > > >
>> > > > > Sincerely,
>> > > > > Michael E. Cotterell
>> > > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
>> > > <[hidden email] (mailto:[hidden email])> wrote:
>> > > > Any ideas?
>> > > >
>> > > > Thanks!
>> > >
>> > > The only way this makes sense to me if is you have a tool with no inputs
>> > > at all (not even an input data file), but it produces one or more output files.
>> > > e.g. "Fetch the human genome as FASTA file, version hg18". But in that
>> > > case you'd be better off just defining the file within a shared data library.
>> > >
>> > > Perhaps you could give an example of the kind of tool you are interested in?
>> > >
>> > > Thanks,
>> > >
>> > > 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/
>> >
>> > 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:
  http://lists.bx.psu.edu/

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Re: Tool Visibility

Michael E. Cotterell
Excellent.  

Is there an example of a modified universe_wsgi.ini file like the one mentioned in the description of the pull request?

Sincerely,
Michael E. Cotterell

Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA & TA, University of Georgia
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
http://michaelcotterell.com/


On Wednesday, June 5, 2013 at 12:11 PM, John Chilton wrote:

> If you look at the date on the pull request it looks like it was a
> full month before they even froze central for the last dist release,
> so at this point I would be more confident it is going to work with
> galaxy-dist than galaxy-central.
>
> -John
>
> On Wed, Jun 5, 2013 at 11:04 AM, Michael E. Cotterell
> <[hidden email] (mailto:[hidden email])> wrote:
> > John,
> >
> > Is there a way to hide an entire section (not just make it greyed out) using the most recent galaxy-dist?
> >
> > I'm investigating the pull request you linked to, and it looks interesting, but is it compatible with galaxy-dist (it's on the bitbucket page for galaxy-central)?
> >
> > Thanks!
> >
> > Sincerely,
> > Michael E. Cotterell
> >
> > Ph.D. Student in Computer Science, University of Georgia
> > Instructor of Record, Graduate RA & TA, University of Georgia
> > [hidden email] (mailto:[hidden email])
> > [hidden email] (mailto:[hidden email])
> > [hidden email] (mailto:[hidden email])
> > http://michaelcotterell.com/
> >
> >
> > On Wednesday, June 5, 2013 at 11:49 AM, John Chilton wrote:
> >
> > > Add workflow_ compatible ="false" to the tool XML element to hide it
> > > in the workflow editor. Check the tools/data_source/upload.xml for an
> > > example of this.
> > >
> > > If you would like to hide it both in the workflow editor and the side
> > > bar but still allow for other direct links to it you can setup dynamic
> > > toolbox filters (you will need to manually pull in the pull request
> > > changes as this has not been merged by the Galaxy team):
> > >
> > > https://bitbucket.org/galaxy/galaxy-central/pull-request/160/implement-dynamic-toolbox-filters
> > >
> > > These can even let you show it to your admins in their side panel, but
> > > not to other users. This way you don't have to hack up the admin
> > > section of the UI.
> > >
> > > Additionally, you may want to go one step further and prevent others
> > > from using the tool (not just preventing them from seeing it). To do
> > > this, you can use dynamic job destinations and prevent these tools
> > > from running for non-admins:
> > >
> > > http://wiki.galaxyproject.org/Admin/Config/Jobs
> > >
> > > -John
> > >
> > >
> > > On Wed, Jun 5, 2013 at 10:37 AM, Michael E. Cotterell
> > > <[hidden email] (mailto:[hidden email])> wrote:
> > > > Peter,
> > > >
> > > > Thanks for getting back to me.
> > > >
> > > > I'm working on an existing project where my predecessors have added a tool that enables a user to add REST and SOAP Web services as usable tools within Galaxy by providing their WSDL or WADL URLs. It makes sense that the tools that are added should show up in both the "Analyze" page and the Workflow editor, but the actual tool for adding Web services is not intended to be used in workflows.
> > > >
> > > > I understand that this tool should probably (more appropriately) be located on the "Admin" page, but in the short run, I'd like to hide this tool from showing up in the list of tools available in the Workflow editor (admittedly, this is the opposite of my original question).
> > > > In the long run, is there an API for adding plugins (or similar) to the admin page? I ask because this particular tool is not designed to be used in a workflow, but rather, it is designed to add tools to Galaxy itself.
> > > >
> > > > Perhaps there is a way to work this into the Toolshed stuff you guys are working on?
> > > >
> > > > Any thoughts are much appreciated.
> > > >
> > > > Thanks!
> > > >
> > > > Sincerely,
> > > > Michael E. Cotterell
> > > >
> > > > Ph.D. Student in Computer Science, University of Georgia
> > > > Instructor of Record, Graduate RA & TA, University of Georgia
> > > > [hidden email] (mailto:[hidden email])
> > > > [hidden email] (mailto:[hidden email])
> > > > [hidden email] (mailto:[hidden email])
> > > > http://michaelcotterell.com/
> > > >
> > > >
> > > > On Wednesday, June 5, 2013 at 11:08 AM, Peter Cock wrote:
> > > >
> > > > > > On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:
> > > > > >
> > > > > > > Suppose a tool didn't have any kind of configuration and therefore didn't
> > > > > > > need to be displayed in the "Analyze Data" part of Galaxy. Is there a way
> > > > > > > to modify tool_conf.xml so that a particular tool is only displayed in the
> > > > > > > Workflow editor?
> > > > > > >
> > > > > > > Thanks!
> > > > > > >
> > > > > > > Sincerely,
> > > > > > > Michael E. Cotterell
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
> > > > > <[hidden email] (mailto:[hidden email])> wrote:
> > > > > > Any ideas?
> > > > > >
> > > > > > Thanks!
> > > > >
> > > > > The only way this makes sense to me if is you have a tool with no inputs
> > > > > at all (not even an input data file), but it produces one or more output files.
> > > > > e.g. "Fetch the human genome as FASTA file, version hg18". But in that
> > > > > case you'd be better off just defining the file within a shared data library.
> > > > >
> > > > > Perhaps you could give an example of the kind of tool you are interested in?
> > > > >
> > > > > Thanks,
> > > > >
> > > > > 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/
> > > >
> > > > 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/