Re: [galaxy-dev] HOWTO share tool parameter settings?
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:jmchil...@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.luka...@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 http://www.pri.wur.nl ___ 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/
Re: [galaxy-dev] HOWTO share tool parameter settings?
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:jmchil...@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.luka...@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 http://www.pri.wur.nl ___ 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/
[galaxy-dev] 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.nlhttp://www.pri.wur.nl/ ___ 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/
