Hi Daniele,

I would suggest having a look at the tools/genomespace/genomespace_importer.py/xml tool, particularly the ‘download_from_genomespace_importer’ method, it uses a comma-separated list of URLs and downloads an adds multiple files to Galaxy, with history names of “GenomeSpace importer on FILENAME”. 

If you don’t need to sniff datatypes, etc, you can ignore those parts.

Thanks for using Galaxy,

Dan

On Apr 16, 2015, at 9:23 AM, John Chilton <jmchilton@gmail.com> wrote:

Yeah - I am not very familiar with data source tools at all - sorry.
Are you creating a galaxy.json file in upload3.py? If you are creating
that file but cannot distinguish between the files - I would try
adding "name" or "designation" fields to the JSON lines in that file -
I would think one of those should work.

-John

On Wed, Apr 1, 2015 at 9:07 AM, Daniele P Colobraro
<d.colobraro@gmail.com> wrote:

Thanks John for your help,
if I get it will I set just a external view of my files?
My idea is to provide multiple files in the galaxy history.
I tried to rewrite the 'galaxy.joson' file but without results.
So far, I have made up just the tool below:

upload3.py $report1 $report1.id $__new_file_path__
#if (len(str($url_paste).split(','))>1):
       #for $i in $url_paste:
               $i
       #end for
#else:
       $url_paste
#end if
</command>
<inputs action="link to" check_values="false" method="post">
      </inputs>
<request_param_translation>
<request_param galaxy_name="URL_method" remote_name="URL_method"
missing="post" />
<request_param galaxy_name="URL" remote_name="URL" missing="" />
<request_param galaxy_name="url_paste" remote_name="mclfile[]" missing="txt"
/>
</request_param_translation>
<outputs>
               <data format="txt" name="report1" />
</outputs>

Using this config file I'm able to import multiple files in the galaxy
history.
But I can't set a name to distinguish them.
I am not sure how to proceed.

If you or anyone have other suggestions I will be grateful.

thanks again
Daniele


2015-03-30 2:57 GMT+02:00 John Chilton <jmchilton@gmail.com>:

There was some work last summer to allow something that at least
vaguely sounds like what you are trying to accomplish - though I was
not involved so I probably am unable to help out much. The Trello card
that was tracking progress on this can be found here -
https://trello.com/c/YlADVbkI - and seems to provide some good
details. I am not sure if there is more formal documentation anywhere
though.

Hope this helps,

-John

On Fri, Mar 27, 2015 at 7:34 AM, Daniele P Colobraro
<d.colobraro@gmail.com> wrote:

Hi all,

I've set up a simple tool using the synchronous method to upload a file
on
galaxy.
I'm able to visit the external link, select and upload a file by the
list.
The script that I use is data_source.py and the 'command' part in the
xml
configuration is the same as the ucsc xml config
(ucsc_tablebrowser.xml).
But my purpose is to import multiple files.

Have you any idea how I can set a way to import/upload multiple files by
using the synchronous method?

Thank in advance,
Best regards
Daniele


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