Hi Björn, thanks, so I just change the format to svg? or is there more to do? The output appears to be empty? Cheers Jochen On 07.02.2017 13:34, Björn Grüning wrote:

Hi Jochen,

svg is supported, see here:

https://github.com/galaxyproject/galaxy/blob/dev/config/datatypes_conf.xml.s...

Cheers, Bjoern

Am 07.02.2017 um 12:45 schrieb Jochen Bick:

...

Hi all,

I'm working on a tool that will have svg as an output file. Is this data type already established? If not how do I start?

Cheers Jochen ___________________________________________________________ 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/

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-- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 Office: Tannenstrasse 1 / TAN D 6.2 8092 Zurich, Switzerland Phone +41 44 632 28 25 jochen.bick@usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch

Just a quick note, if you want svg to be rendered as a graphics correctly via the eye preview, you’ll need to set “serve_xss_vulnerable_mimetypes = True" in galaxy.ini. Otherwise it will appear as plaintext xml. But do be aware of the security concerns if you change this setting. Downloading/saving the svg and then manually opening will work regardless. Thanks for using Galaxy, Dan

On Feb 7, 2017, at 3:17 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:

Hi,

just change it to svg. If the output is empty this could be a tool problem.

Ciao, Bjoern

Am 07.02.2017 um 14:19 schrieb Jochen Bick:

...

Hi Björn,

thanks, so I just change the format to svg? or is there more to do? The output appears to be empty?

Cheers Jochen

On 07.02.2017 13:34, Björn Grüning wrote:

...

Hi Jochen,

svg is supported, see here:

https://github.com/galaxyproject/galaxy/blob/dev/config/datatypes_conf.xml.s...

Cheers, Bjoern

Am 07.02.2017 um 12:45 schrieb Jochen Bick:

...

Hi all,

I'm working on a tool that will have svg as an output file. Is this data type already established? If not how do I start?

Cheers Jochen ___________________________________________________________ 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/

Hi Jochen, I’m not sure I follow exactly. The SVG format is basically an XML file that can be visualized as a graphic. Whether it will be displayed as a graphic within your browser or as text generally depends upon the mime type that is set. If the mime type is set as text/plain, it will render as plain text, if it is set as image/svg+xml it will be rendered as an image; the previously mentioned flag will control which is used for this datatype. However, the actual file contents are the same. Dan

On Feb 8, 2017, at 2:46 AM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:

Thanks Dan,

I would like to have it as plain text but no as a separate file in the history but more like the solution of bam and bai files. Do you know how to do that?

Cheers Jochen

On 07.02.2017 21:26, Daniel Blankenberg wrote:

...

Just a quick note, if you want svg to be rendered as a graphics correctly via the eye preview, you’ll need to set “serve_xss_vulnerable_mimetypes = True" in galaxy.ini. Otherwise it will appear as plaintext xml. But do be aware of the security concerns if you change this setting. Downloading/saving the svg and then manually opening will work regardless.

Thanks for using Galaxy,

Dan

Hmm. I wonder if a composite datatype would work here? https://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes Peter On Thu, Feb 9, 2017 at 9:25 AM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:

Hi Dan,

I understand the option with this specific flag. What I mean is that for example the file format bam has two file in one save button. So if you click on save you can either save the bam file or the bai file. I would liek to have the same feature with my png and svg. So that I have just one item in the history showing the png and if you click on save you have the option to also save svg.

Cheers Jochen ___________________________________________________________ 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/

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