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 <marten@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 <dokadya@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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