Re: [galaxy-dev] Loading tool config file
Yes this does help thanks Dannon!:) On Fri, Jul 22, 2016 at 8:08 AM, Dannon Baker wrote: > Hi Katherine, > > This all happens in javascript these days, and it's unfortunately a little > harder to track down all the moving parts than it used to be when this was > all rendered serverside. The client requests tool information (like which > parameters are necessary, etc) from the API, which it then renders using > the primary tool form found here: > > https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/mvc/tool > > This extends the form code found here: > > https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/mvc/form > > And individual element types (a select box, for example) can be found here: > > https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/mvc/ui > > Does this help? > > > On Fri, Jul 22, 2016 at 7:40 AM Peter Cock > wrote: > >> Sorry, I know relatively little about how Galaxy loads the tool XML >> files and turns this into the HTML pages. I've mostly searched >> the codebase with grep at the command line (also searching >> directly on GitHub works pretty well) trying to trace functionality >> when I was debugging something. >> >> Hopefully one of the Galaxy developers will be able to answer. >> >> Peter >> >> >> On Fri, Jul 22, 2016 at 7:29 AM, Katherine Beaulieu wrote: >> > >> > No I'm really asking about which files in Galaxy, will load those >> > parameters on the screen. I believe you were the one to give me a link >> to >> > adding a new parameter type in Galaxy via the password parameter, but I >> > haven't quite been able to implement that. The two files I have changed >> so >> > far are basic.py and form_builder.py but using these two files it still >> only >> > loads a text parameter. >> ___ >> 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Loading tool config file
Hi Katherine, This all happens in javascript these days, and it's unfortunately a little harder to track down all the moving parts than it used to be when this was all rendered serverside. The client requests tool information (like which parameters are necessary, etc) from the API, which it then renders using the primary tool form found here: https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/mvc/tool This extends the form code found here: https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/mvc/form And individual element types (a select box, for example) can be found here: https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/mvc/ui Does this help? On Fri, Jul 22, 2016 at 7:40 AM Peter Cock wrote: > Sorry, I know relatively little about how Galaxy loads the tool XML > files and turns this into the HTML pages. I've mostly searched > the codebase with grep at the command line (also searching > directly on GitHub works pretty well) trying to trace functionality > when I was debugging something. > > Hopefully one of the Galaxy developers will be able to answer. > > Peter > > > On Fri, Jul 22, 2016 at 7:29 AM, Katherine Beaulieu wrote: > > > > No I'm really asking about which files in Galaxy, will load those > > parameters on the screen. I believe you were the one to give me a link to > > adding a new parameter type in Galaxy via the password parameter, but I > > haven't quite been able to implement that. The two files I have changed > so > > far are basic.py and form_builder.py but using these two files it still > only > > loads a text parameter. > ___ > 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Loading tool config file
No I have not sorry. On Fri, Jul 22, 2016 at 7:43 AM, Mohamed Kassam wrote: > Hello Katherine, > it is Mohamed from the NIHS. > So have you find a way to incluse the password tahg in the xml file ? > > Mohamed > > 2016-07-22 13:34 GMT+02:00 Katherine Beaulieu < > katherine.beaulieu...@gmail.com>: > >> >> >> On Fri, Jul 22, 2016 at 7:29 AM, Katherine Beaulieu < >> katherine.beaulieu...@gmail.com> wrote: >> >>> No I'm really asking about which files in Galaxy, will load those >>> parameters on the screen. I believe you were the one to give me a link to >>> adding a new parameter type in Galaxy via the password parameter, but I >>> haven't quite been able to implement that. The two files I have changed so >>> far are basic.py and form_builder.py but using these two files it still >>> only loads a text parameter. >>> >>> On Fri, Jul 22, 2016 at 7:26 AM, Peter Cock >>> wrote: >>> Hi Katherine, Are you asking about the XML files which described Galaxy Tools by listing all the options to show the user, any help text to show the user, and instructions for how to turn the options picked into a command line to be executed: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter On Fri, Jul 22, 2016 at 12:09 PM, Katherine Beaulieu wrote: > Dear all, > I am looking for the files/functions that get called from the point where > you click on the tool name to the point where you get an html version of > your tool on the screen. Could someone indicate what this path looks like? I > would be really appreciative! > Thanks, > Katherine > > ___ > 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: >> 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Loading tool config file
Sorry, I know relatively little about how Galaxy loads the tool XML files and turns this into the HTML pages. I've mostly searched the codebase with grep at the command line (also searching directly on GitHub works pretty well) trying to trace functionality when I was debugging something. Hopefully one of the Galaxy developers will be able to answer. Peter On Fri, Jul 22, 2016 at 7:29 AM, Katherine Beaulieu wrote: > > No I'm really asking about which files in Galaxy, will load those > parameters on the screen. I believe you were the one to give me a link to > adding a new parameter type in Galaxy via the password parameter, but I > haven't quite been able to implement that. The two files I have changed so > far are basic.py and form_builder.py but using these two files it still only > loads a text parameter. ___ 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/
Re: [galaxy-dev] Loading tool config file
On Fri, Jul 22, 2016 at 7:29 AM, Katherine Beaulieu < katherine.beaulieu...@gmail.com> wrote: > No I'm really asking about which files in Galaxy, will load those > parameters on the screen. I believe you were the one to give me a link to > adding a new parameter type in Galaxy via the password parameter, but I > haven't quite been able to implement that. The two files I have changed so > far are basic.py and form_builder.py but using these two files it still > only loads a text parameter. > > On Fri, Jul 22, 2016 at 7:26 AM, Peter Cock > wrote: > >> Hi Katherine, >> >> Are you asking about the XML files which described Galaxy Tools >> by listing all the options to show the user, any help text to show the >> user, and instructions for how to turn the options picked into a >> command line to be executed: >> >> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax >> >> Peter >> >> On Fri, Jul 22, 2016 at 12:09 PM, Katherine Beaulieu >> wrote: >> > Dear all, >> > I am looking for the files/functions that get called from the point >> where >> > you click on the tool name to the point where you get an html version of >> > your tool on the screen. Could someone indicate what this path looks >> like? I >> > would be really appreciative! >> > Thanks, >> > Katherine >> > >> > ___ >> > 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Loading tool config file
Hi Katherine, Are you asking about the XML files which described Galaxy Tools by listing all the options to show the user, any help text to show the user, and instructions for how to turn the options picked into a command line to be executed: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter On Fri, Jul 22, 2016 at 12:09 PM, Katherine Beaulieu wrote: > Dear all, > I am looking for the files/functions that get called from the point where > you click on the tool name to the point where you get an html version of > your tool on the screen. Could someone indicate what this path looks like? I > would be really appreciative! > Thanks, > Katherine > > ___ > 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Loading tool config file
Dear all, I am looking for the files/functions that get called from the point where you click on the tool name to the point where you get an html version of your tool on the screen. Could someone indicate what this path looks like? I would be really appreciative! Thanks, Katherine ___ 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/
