Hi Daniel and John, thanks a lot for your replies. I have tried creating a galaxy.json file, but I haven't had much time, so I gave up that. But I am interested to use your suggestions. For my solution, I followed the explanations in:
https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files https://bitbucket.org/galaxy/galaxy-central/src/default/test/functional/tools/multi_output_configured.xml So, I am able to visit my remote web page, select which items I want (with a check-box form) and upload them to galaxy. As advised in multi_output_configured.xml, I create the subdir in my python script by using os.mkdir('subdir1'). But I am going to create a more elegant solution. Thanks again for your replies, I'll exploit them soon. Daniele 2015-04-16 16:01 GMT+02:00 Daniel Blankenberg <d...@bx.psu.edu>: > 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 <jmchil...@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.colobr...@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 <jmchil...@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.colobr...@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 > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > >
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