On Thu, Sep 21, 2017 at 12:50 PM, SAPET, Frederic <frederic.sapet@biogemma.com> wrote:
Hi Peter,

Good idea, I will keep that in mind for other needs.
I'm not sure that it will be suitable for what I want to do. Users will have to first import database to their history (yet another step as they ask me for less, even the upload process is sometimes one step they would like to avoid !) 
 
But it could be a way of achieving what I want, if Galaxy could get files (or .loc files) from a data library, within the tool form itself ! 
 
Maybe I will create an issue on the Galaxy git in order to discuss about that. I will be glad to help if something can be done.

Good idea! I wonder if the Galaxy UI team can think of a good way to integrate this, which would make Shared Data library files available to any tool without the import to current history step? Can you reply with a link to the new GitHub issue for this?
 
Maybe some explanations about the fact that my users ask me for "less steps".
I really want Galaxy to be the main tool of our analysis platform.
Right now I still maintain a plain old perl/php/CGI web interface. With a blast tool (among a lot of others tools). This proprietary Blast interface is really like you will find on NCBI or EBI sites. And you can quickly paste your sequences, pick up a database, a Blast algorythm and then launch. Few seconds later I have a 'htmlized' Blast report, with a nice picture.
This use case (is this sequence a part of this database ?) is still faster on this plain old interface. And I afraid that I will have to keep it until they found Galaxy better than it...

We used to run wwwBLAST locally for similar reasons. If I was trying to setup up something similar now, I'd look at http://www.sequenceserver.com/ for this - but making the Galaxy alternative easier to use would be neater.
 
Maybe it could be another (or two) idea(s)  : the user can drag and drop his file within the tool form, Galaxy will handle the creation of this file within the history and then launch the tool. Or user can copy/paste a sequence within a text-area, and Galaxy will handle the creation of a file from these data within the history and then launch the tool.
This skips upload process.

The Galaxy upload does now support drag and drop, so again in principle the Galaxy team might be able to extend the tool interface as well. The tool input's expected file formats could be used to guide the data-type sniffer and/or short list the choices shown to the use.

As well or instead, I could imagine having an upload icon associated with each tool input (again, creating a history item and selecting it for you)? This could take advantage of the fact that each tool's input parameter specifies the expected input file formats, so that might be mapped to known file extensions for a file picker?
 

thank you again for sharing your ideas, it helps!

Fred

These are great usability ideas you are putting forward here - as a Galaxy Tool Author they sound positive, but I cannot comment on how complicated it would be for the Galaxy UI team. Or indeed if the UI would actually be practical - or just overly complicate things which is always a risk.

Peter