2010/2/25 Anton Nekrutenko <anton@bx.psu.edu>

Jelle:

The main issue with this is that is your blast output is 500Mb (which is very common) the browser will have a hard time dealing with it even if there is an editor. Isn't filter tool sufficient to help with irregularities?

a.

On Feb 25, 2010, at 1:17 AM, Jelle Scholtalbers wrote:

Hans,

most cases are indeed solved with the tools already available, removing a line from the top was a bad example :) . However if you have a blast result that you don't want to filter on any particular score, but you want to judge by the alignment and the combination of the different scorings after which you want to filter out several lines which don't have any obvious regularity, then a text editor is the simplest solution.

I understand that a texteditor is maybe not the best way for getting a clear history, however the other alternative is to get it out of galaxy and do it on your desktop and place it back in. If there is a tool in galaxy it will all stay in galaxy and just with any other tool, when the file is saved a new file is generated and the original remains. If you then want to see the differences between the files you could do a diff.

Cheers,
Jelle

2010/2/24 Hotz, Hans-Rudolf <hrh@fmi.ch>
Jelle

> sometimes after uploading a file I will see an error which is very minor,
> say a header of a column has a space in it where it shouldn't have one. Or a
> extra line is added in the top of the file which I don't need.

Have you tried working with the tools from the "Text Manipulation"?

ie. "Remove beginning of a file" alone or in combination with "Concatenate
queries tail-to-head" will probably solve most of your cases in just a few
steps.

Regards, Hans

> This can also happen after I run a tool and the result I get is ok, but I
> want to edit the result before it goes to the next tool. For a workflow this
> is probably not what you want, but for some basic analysis or 'playing
> around' it can become very handy to have.
>
> So it is mostly about very small edits, mostly fixing typing errors or
> removing one or a few lines.
>
> Cheers,
> Jelle
>
> 2010/2/24 Anton Nekrutenko <anton@bx.psu.edu>
>
>> Jelle:
>>
>> CAn you tell us a bit more about the types of edits you are doing?
>>
>> Tx,
>> anton
>>
>>
>>
>> On Feb 24, 2010, at 10:18 AM, Jelle Scholtalbers wrote:
>>
>> Hi,
>>>
>>> is there a possibility to have a very basic text editor within Galaxy (or
>>> is there already one and I didn't find it)? I find myself saving files to my
>>> pc and uploading them again, or use some regular expression to edit my
>>> files, just to fix some small part that needs to be edited before it can go
>>> into a tool. Enabling a text editor for files not larger as they are
>>> provided by the 'display data' would be very helpful.
>>>
>>> Cheers,
>>> Jelle
>>> _______________________________________________
>>> galaxy-user mailing list
>>> galaxy-user@lists.bx.psu.edu
>>> http://lists.bx.psu.edu/listinfo/galaxy-user
>>>
>>
>> Anton Nekrutenko
>> http://nekrut.bx.psu.edu
>> http://usegalaxy.org
>>
>>
>>
>>
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