forwarding to the list ---------- Forwarded message --------- From: Katherine Beaulieu <katherine.beaulieu014@gmail.com> Date: Fri, Jul 15, 2016 at 3:45 PM Subject: Re: [galaxy-dev] New galaxy parameter type To: Martin Čech <marten@bx.psu.edu> Thanks Peter, I will look into that. The reason I am asking is because of what Mohammed asked earlier as well. I developed two tools which allow you to import and export information from a program called irods but you need to be able to authenticate with irods to be able to do so. Thanks again for always being helpful! On Fri, Jul 15, 2016 at 3:10 PM, Martin Čech <marten@bx.psu.edu> wrote:
Katherine please disregard my answer, I probably misread your question. :) M.
On Fri, Jul 15, 2016 at 3:05 PM Peter Cock <p.j.a.cock@googlemail.com> wrote:
Did you mean parameter as in input field shown to the user? Like a combobox or text field?
Since this happened to come up earlier today, here's a rejected pull request which added a password parameter - that ought to give you a rough idea:
https://github.com/galaxyproject/galaxy/pull/393
Peter
On Fri, Jul 15, 2016 at 7:46 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hi everyone, I am looking to implement a new parameter type for galaxy tool development. Does anyone know what would be involved in doing something like this or perhaps what files would need to be edited?
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Dear all, I did not want to open a new subject, because I have the same problem. I tried to follow what is was described here https://github.com/galaxyproject/galaxy/pull/393, I add the lines a described in the github, but when I am clicking to my tool I got [image: Images intégrées 1] And if i check the error in commad line I have galaxy.web.framework.decorators ERROR 2016-07-20 10:05:44,357 Uncaught exception in exposed API method: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py", line 258, in decorator rval = func( self, trans, *args, **kwargs) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/tools.py", line 100, in build return tool.to_json(trans, kwd.get('inputs', kwd)) File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2383, in to_json populate_state(trans, self.inputs, state_inputs, state_errors, params.__dict__) File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2255, in populate_state state[input.name] = input.get_initial_value(trans, context, history=history) TypeError: get_initial_value() got an unexpected keyword argument 'history' 10.38.149.37 - - [20/Jul/2016:10:05:44 +0200] "GET /api/tools/irods_pull_main/build HTTP/1.1" 500 - "http://10.38.152.152:8080/" "Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36" Maybe something to add for the new version of galaxy ? Thanks in advance, Mohamed 2016-07-15 21:54 GMT+02:00 Martin Čech <marten@bx.psu.edu>:
forwarding to the list
---------- Forwarded message --------- From: Katherine Beaulieu <katherine.beaulieu014@gmail.com> Date: Fri, Jul 15, 2016 at 3:45 PM Subject: Re: [galaxy-dev] New galaxy parameter type To: Martin Čech <marten@bx.psu.edu>
Thanks Peter, I will look into that. The reason I am asking is because of what Mohammed asked earlier as well. I developed two tools which allow you to import and export information from a program called irods but you need to be able to authenticate with irods to be able to do so. Thanks again for always being helpful!
On Fri, Jul 15, 2016 at 3:10 PM, Martin Čech <marten@bx.psu.edu> wrote:
Katherine please disregard my answer, I probably misread your question. :) M.
On Fri, Jul 15, 2016 at 3:05 PM Peter Cock <p.j.a.cock@googlemail.com> wrote:
Did you mean parameter as in input field shown to the user? Like a combobox or text field?
Since this happened to come up earlier today, here's a rejected pull request which added a password parameter - that ought to give you a rough idea:
https://github.com/galaxyproject/galaxy/pull/393
Peter
On Fri, Jul 15, 2016 at 7:46 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hi everyone, I am looking to implement a new parameter type for galaxy tool development. Does anyone know what would be involved in doing something like this or perhaps what files would need to be edited?
___________________________________________________________ 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/
participants (2)
-
Martin Čech -
Mohamed Kassam