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Create a new datatype svg

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Create a new datatype svg

Jochen
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
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Re: Create a new datatype svg

Björn Grüning-3
Hi Jochen,

svg is supported, see here:

https://github.com/galaxyproject/galaxy/blob/dev/config/datatypes_conf.xml.sample#L282

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/
>
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Re: Create a new datatype svg

Jochen
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.sample#L282
>
> 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/
>>

--
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
[hidden email] <mailto:[hidden email]>
www.ap.ethz.ch
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Re: Create a new datatype svg

Björn Grüning-3
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.sample#L282
>>
>> 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/
>>>
>
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Re: Create a new datatype svg

Daniel Blankenberg
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 <[hidden email]> 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.sample#L282

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
___________________________________________________________
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Re: Create a new datatype svg

Jochen
In reply to this post by Björn Grüning-3
Hej Björn,

ok you were right... I had a tool issue.
Now its working.

Cheers Jochen

On 07.02.2017 21:17, Björn Grüning wrote:
> Hi,
>
> just change it to svg. If the output is empty this could be a tool problem.
>
> Ciao,
> Bjoern
>
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Re: Create a new datatype svg

Jochen
In reply to this post by Daniel Blankenberg
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
>

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Re: Create a new datatype svg

Daniel Blankenberg
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 <[hidden email]> 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
>>
>

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Re: Create a new datatype svg

Jochen
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
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Re: Create a new datatype svg

Peter Cock
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 <[hidden email]> 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/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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