HOWTO share tool parameter settings?
Hi, Do we have a way (or plans) for sharing tool parameter settings in Galaxy? I know the following workarounds : * Share a history with all users: so users can import your step and do "rerun" to run on their own file with your settings * Wrap the step in a workflow with all parameters set and publish this workflow: users can run this "workflow" * Have a dummy tool to produce a settings file and allow the users to choose this file when running the real tool * Use a conditional and many macros that are basically a copy of each other, only differing in the parameter values But what I would like to have is a way to define bindings between a settings file and the parameters in the tool form. Any plans, ideas? Thanks, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>
How would this be different then the third option you listed? You want it to work with all tools and you as the developer want to be able to construct these files without needing a dummy tool to produce the values? How would imagine these setting files would be disseminated to users and then selected by users? -John On Thu, Oct 9, 2014 at 9:34 AM, Lukasse, Pieter <pieter.lukasse@wur.nl> wrote:
Hi,
Do we have a way (or plans) for sharing tool parameter settings in Galaxy?
I know the following workarounds :
· Share a history with all users: so users can import your step and do “rerun” to run on their own file with your settings
· Wrap the step in a workflow with all parameters set and publish this workflow: users can run this “workflow”
· Have a dummy tool to produce a settings file and allow the users to choose this file when running the real tool
· Use a conditional and many macros that are basically a copy of each other, only differing in the parameter values
But what I would like to have is a way to define bindings between a settings file and the parameters in the tool form. Any plans, ideas?
Thanks,
Pieter Lukasse
Wageningen UR, Plant Research International
Department of Bioinformatics (Bioscience)
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur
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Hi John, The difference with an external "settings-only" file and the third option is that the last one has settings and layout mixed up. Say we want to change the order of two fields in a form, then with the macros approach I would need to change N macro files for N different versions (each version related to different set of parameter values). I could use the <token> option if it would allow for conditionally loading a different sets of token values, depending of e.g. a select box option by the user. I hope it is somewhat clearer now, but do not hesitate to send me more questions! Best regards, Pieter. -----Original Message----- From: John Chilton [mailto:jmchilton@gmail.com] Sent: donderdag 9 oktober 2014 15:45 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] HOWTO share tool parameter settings? How would this be different then the third option you listed? You want it to work with all tools and you as the developer want to be able to construct these files without needing a dummy tool to produce the values? How would imagine these setting files would be disseminated to users and then selected by users? -John On Thu, Oct 9, 2014 at 9:34 AM, Lukasse, Pieter <pieter.lukasse@wur.nl> wrote:
Hi,
Do we have a way (or plans) for sharing tool parameter settings in Galaxy?
I know the following workarounds :
· Share a history with all users: so users can import your step and do “rerun” to run on their own file with your settings
· Wrap the step in a workflow with all parameters set and publish this workflow: users can run this “workflow”
· Have a dummy tool to produce a settings file and allow the users to choose this file when running the real tool
· Use a conditional and many macros that are basically a copy of each other, only differing in the parameter values
But what I would like to have is a way to define bindings between a settings file and the parameters in the tool form. Any plans, ideas?
Thanks,
Pieter Lukasse
Wageningen UR, Plant Research International
Department of Bioinformatics (Bioscience)
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur
___________________________________________________________ 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/
Hi John, I see that in my last email I replied to you with the fourth (and not the third) option in mind :(. Just to come back to this related to the third option (i.e. " Have a dummy tool to produce a settings file and allow the users to choose this file when running the real tool"): I don't like this option so much because the file is never as clear as the tool form that produced it. If users are used to looking at the tool form for seeing details about the set parameters and now they will have to look at a text file, this will be confusing. It is not a huge problem, but it is one that I am trying to avoid. I.e. it would be best if users are presented with only one way of checking parameters of executed processes. In the scenario I am proposing, the settings files are disseminated just as they are (e.g. a text file) either by sharing them in the normal ways or by placing a number of them in pre-defined folders in Galaxy. The tool form would allow the user to select one and would then fill in the values of the parameters accordingly. I'm guessing similar binding logic is also happening right now when a user clicks "rerun" on a step in his history. Best regards, Pieter. -----Original Message----- From: John Chilton [mailto:jmchilton@gmail.com] Sent: donderdag 9 oktober 2014 15:45 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] HOWTO share tool parameter settings? How would this be different then the third option you listed? You want it to work with all tools and you as the developer want to be able to construct these files without needing a dummy tool to produce the values? How would imagine these setting files would be disseminated to users and then selected by users? -John On Thu, Oct 9, 2014 at 9:34 AM, Lukasse, Pieter <pieter.lukasse@wur.nl> wrote:
Hi,
Do we have a way (or plans) for sharing tool parameter settings in Galaxy?
I know the following workarounds :
· Share a history with all users: so users can import your step and do “rerun” to run on their own file with your settings
· Wrap the step in a workflow with all parameters set and publish this workflow: users can run this “workflow”
· Have a dummy tool to produce a settings file and allow the users to choose this file when running the real tool
· Use a conditional and many macros that are basically a copy of each other, only differing in the parameter values
But what I would like to have is a way to define bindings between a settings file and the parameters in the tool form. Any plans, ideas?
Thanks,
Pieter Lukasse
Wageningen UR, Plant Research International
Department of Bioinformatics (Bioscience)
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur
___________________________________________________________ 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/
Pieter - Sorry for the delay - I am not sure how to respond - but I am trying to get through my e-mail backlog before winter break. I think this could be kind of cool - stuff has been added to the top of that tool run screen lately and probably more will be added soon. I think an option to basically take the JSON that an API request would take and populate the form would be possible and a lot easier now that Sam has rewritten the form in JavaScript so everything can be more easily dynamic. We had a tool developer meeting (which we probably should have announced here on -dev instead of just on github in retrospect) and one of the ideas that came out of that was the option to take an existing tool run and basically extract a tool test XML block to stick into the tool - I imagine the mechanism for doing tool parameter sets could be similar. It would also be something useful for disseminating say properties in papers that is lighter than whole workflows or histories. So I like it - but it is probably not a top priority for the devteam at this time - happy to review pull requests though of course. -John On Thu, Oct 16, 2014 at 4:15 AM, Lukasse, Pieter <pieter.lukasse@wur.nl> wrote:
Hi John,
I see that in my last email I replied to you with the fourth (and not the third) option in mind :(.
Just to come back to this related to the third option (i.e. " Have a dummy tool to produce a settings file and allow the users to choose this file when running the real tool"): I don't like this option so much because the file is never as clear as the tool form that produced it. If users are used to looking at the tool form for seeing details about the set parameters and now they will have to look at a text file, this will be confusing. It is not a huge problem, but it is one that I am trying to avoid. I.e. it would be best if users are presented with only one way of checking parameters of executed processes.
In the scenario I am proposing, the settings files are disseminated just as they are (e.g. a text file) either by sharing them in the normal ways or by placing a number of them in pre-defined folders in Galaxy. The tool form would allow the user to select one and would then fill in the values of the parameters accordingly. I'm guessing similar binding logic is also happening right now when a user clicks "rerun" on a step in his history.
Best regards,
Pieter.
-----Original Message----- From: John Chilton [mailto:jmchilton@gmail.com] Sent: donderdag 9 oktober 2014 15:45 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] HOWTO share tool parameter settings?
How would this be different then the third option you listed?
You want it to work with all tools and you as the developer want to be able to construct these files without needing a dummy tool to produce the values?
How would imagine these setting files would be disseminated to users and then selected by users?
-John
On Thu, Oct 9, 2014 at 9:34 AM, Lukasse, Pieter <pieter.lukasse@wur.nl> wrote:
Hi,
Do we have a way (or plans) for sharing tool parameter settings in Galaxy?
I know the following workarounds :
· Share a history with all users: so users can import your step and do “rerun” to run on their own file with your settings
· Wrap the step in a workflow with all parameters set and publish this workflow: users can run this “workflow”
· Have a dummy tool to produce a settings file and allow the users to choose this file when running the real tool
· Use a conditional and many macros that are basically a copy of each other, only differing in the parameter values
But what I would like to have is a way to define bindings between a settings file and the parameters in the tool form. Any plans, ideas?
Thanks,
Pieter Lukasse
Wageningen UR, Plant Research International
Department of Bioinformatics (Bioscience)
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur
___________________________________________________________ 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/
participants (2)
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John Chilton -
Lukasse, Pieter