Thank you very much Martin Čech for reply.
Currently I am uploading data by using linking method only,
But what I wanted is NO API, that means via terminal only.

As you can see my first mail where I am explaining query,
MuSiC2 creating folders and files by itself, and hence galaxy will not be
able to track those files.
hence I want to collect those files and upload to current history (as data
sets) using Terminal.
Is that thing is possible ?

else how can I tell Galaxy that tool is creating folder first and then
writing files ?
I am using    http://cli-mate.lumc.nl/define#    to create xml file for
galaxy.
I know I can hide output (from main command), but how can i track file
which is inside folder ?

Waiting for positive reply.

On Tue, Mar 25, 2014 at 6:04 PM, Martin Čech <mar...@bx.psu.edu> wrote:

> Hi,
>
> yes, you can link files to a Galaxy Library without copying -  please see
> https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles(the 
> last part 'Upload files from filesystem paths').
>
> And there is an API for libraries (although it is under construction). The
> flow of controllers for upload is api/library_contents >
> controllers/library_common
>
>
> https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.library_contents
>
> Martin
>
>
> On Tue, Mar 25, 2014 at 7:47 AM, do kadya <doka...@gmail.com> wrote:
>
>> Hi,
>> Can I upload data (mostly link the data) using terminal ?
>>
>> MuSiC 2 tool integration is not available in their website nor in tool
>> shed.
>> MuSiC 2 creates folder and files by itself, which is hard to track by
>> Galaxy.
>>
>> So is there any way to link files to galaxy current work space so that I
>> can link those distracted files which are created by MuSiC 2.
>>
>> ex: if you run
>>                 music2   bmr     calc-bmr    file_of_input
>>
>> output is 3 files,
>> ./file1.txt
>> ./folder1/file2.txt
>> ./folder2/file3.txt
>> we can not mention that we need this output filename or save file at
>> specific location, we can not give this option.
>>
>>
>> Galaxy will not able to track this output, hence i have to do it
>> manually. So is it possible to upload this files manually by terminal ?
>>
>>
>>
>>
>> Waiting for positive reply.
>> Thank You
>> - Chetan
>>
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