Re: [galaxy-dev] making tools with Galaxy
Hello Lionel, Please send correspondence like this to the galaxy-dev@lists.bx.psu.edu mailing list rather than individual email accounts as doing so will ensure more timely and optimal repoonses. I'm not quite sure what code you are reading, so could you please clarify? In general, though, when you write a Galaxy wrapper to integrate a tool into Galaxy, you will be able to load the tool into the Galaxy tool panel, and the tool UI will display in the main Galaxy panel. When you execute the tool, a Galaxy job will get created which will produce an output in the form of a dataset. This dataset will be displayed in you Galaxy history as the result of excuting the tool. So, in your case, the history item will include the png file and, when clicked , it should display in your main Galaxy panel. There are a lot of details that are calrified in the Galaxy wiki - a good place to start is probably: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Greg Von Kuster On Jan 16, 2014, at 5:56 AM, Lionel Chiron <lionel.chiron@nmrtec.com> wrote:
Hi Greg,
I'm trying to make a tool in Galaxy for implementing our algorithm for mass spectrometry treatment but it is a little tricky for me.. To make run the algorithm in Python is ok, I produce a png with matplotlib .. but after that I 'm a little lost since I don't know where the picture is produced.. reading your code I can't figure out how you indicate where to produce the png file.. How can I do?? Thanks
Lionel
Hi Lionel, here is a simple example of an graphicsmagic wrapper, that consumes an image and produce one. Maybe its useful for you. https://github.com/bgruening/galaxytools/tree/master/image_processing Cheers, Bjoern
Hello Lionel,
Please send correspondence like this to the galaxy-dev@lists.bx.psu.edu mailing list rather than individual email accounts as doing so will ensure more timely and optimal repoonses.
I'm not quite sure what code you are reading, so could you please clarify?
In general, though, when you write a Galaxy wrapper to integrate a tool into Galaxy, you will be able to load the tool into the Galaxy tool panel, and the tool UI will display in the main Galaxy panel. When you execute the tool, a Galaxy job will get created which will produce an output in the form of a dataset. This dataset will be displayed in you Galaxy history as the result of excuting the tool. So, in your case, the history item will include the png file and, when clicked , it should display in your main Galaxy panel.
There are a lot of details that are calrified in the Galaxy wiki - a good place to start is probably:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Greg Von Kuster
On Jan 16, 2014, at 5:56 AM, Lionel Chiron <lionel.chiron@nmrtec.com> wrote:
Hi Greg,
I'm trying to make a tool in Galaxy for implementing our algorithm for mass spectrometry treatment but it is a little tricky for me.. To make run the algorithm in Python is ok, I produce a png with matplotlib .. but after that I 'm a little lost since I don't know where the picture is produced.. reading your code I can't figure out how you indicate where to produce the png file.. How can I do?? Thanks
Lionel
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participants (2)
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Björn Grüning -
Greg Von Kuster