Hello, Shashi

It looks like TreeViewX was written in C++ as a desktop program. In this case, there is no way that it can be used with the display_application code without major modification.

One option is to not use TreeViewX from within Galaxy but simply have it installed on your users' computers and have them load their Galaxy data into it after downloading to their local machines.

Other options may include other phylogenetic tree viewers and formatters. There are many excellent programs and libraries available:
FigTree http://tree.bio.ed.ac.uk/software/figtree/
Archaeopteryx https://sites.google.com/site/cmzmasek/home/software/archaeopteryx
and jsPhyloSVG (javascript) http://www.jsphylosvg.com/

If you need to produce phylogenetic trees within Galaxy, the phyloviz visualization is the best place for you to start. In order to modify it to get the features you'd need from it, however, you'll need to have some experience with programming in JavaScript, python, and a web development environment. There are many resources on the internet to help you.

We'd like to add to add functionality to phyloviz at some point (such as saving to SVG, re-formatting the trees, etc.) so, if you're not able, we will be working on it. However, those improvements may not be done anytime soon.


On Thu, Jun 20, 2013 at 7:36 AM, shashi shekhar <me_shashi29@yahoo.co.in> wrote:
Hi Ross,

i am using display application as  visualization in galaxy.

display id="ucsc_interval_as_bed" version="1.0.0" name="display at UCSC">
    <link id="main" name="main">
        <url>http://genome.ucsc.edu/cgi-bin/hgTracks?db=${qp($bed_file.dbkey)}&amp;position=${position.qp}&amp;hgt.customText=${bed_file.qp}</url>
        <param type="data" name="bed_file" url="galaxy.bed" format="bedstrict"/> <!-- Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, UCSC does not: force use of converter which will make strict BED6+ file -->
        <param type="template" name="position" strip="True" >

what is the meaninng  <param type="template" name="position" strip="True" />
and what is the use of url="galaxy.bed" ?



Regards
shashi
From: Ross <ross.lazarus@gmail.com>
To: shashi shekhar <me_shashi29@yahoo.co.in>
Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Sent: Wednesday, 19 June 2013 5:32 PM

Subject: Re: [galaxy-dev] visulaization tool

Shashi,
Beats me. Cloning the visualisation code would be a good start I'd guess. It will not be trivial.
Others may have better ideas.

On Wed, Jun 19, 2013 at 9:56 PM, shashi shekhar <me_shashi29@yahoo.co.in> wrote:
Hi Ross,
Actually i have to add the  visualization which  will be interactive . it  will take dataset  from galaxy .it will be in the same way as tracker works .
in stead of tracker i want to add my own visualization tool. from wehere should i start  to replace tracker with my own visulization tool.
Regards
shashi

Sent: Wednesday, 19 June 2013 5:02 PM

Subject: Re: [galaxy-dev] visulaization tool

Shashi,
Thanks for the additional information. 
AFAIK: If it's command line driven and spews out pdf's, adapt any similar tool that spews out pdfs like fastqc. 
Galaxy tool execution is isolated from the user and from Galaxy itself, so communication is just not possible if it's interactive - unless you hack the tool into Galaxy itself or something. There is no documentation for that.



On Wed, Jun 19, 2013 at 9:01 PM, shashi shekhar <me_shashi29@yahoo.co.in> wrote:
Hi Ross,
thanks for the reply . actually i want to use TreeView as visulaization tool.

TreeView X is an open source and multi-platform program to display phylogenetic trees. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It allows one to order the branches of the trees, and to export the trees in SVG format.

i have to add  treeviewx in galaxy..

Regards
shashi


From: Ross <ross.lazarus@gmail.com>
To: shashi shekhar <me_shashi29@yahoo.co.in>
Cc: Hans-Rudolf Hotz <hrh@fmi.ch>; "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Sent: Wednesday, 19 June 2013 3:28 PM

Subject: Re: [galaxy-dev] visulaization tool

Shashi,
Hans made a brave guess based on your vague question, but you'll probably get better answers if you do us all a favour and make an effort to provide unambiguous detail about exactly what you want to achieve. 

If there is a working Galaxy tool that does what you need but using a different "visualisation program" (whatever you mean by that vague term), substituting your executable will probably be relatively trivial. eg do you consider the Html object produced by the fastqc or the image from the scatterplot tool to be "visualisation program" outputs? If so, clone a working tool.


On Wed, Jun 19, 2013 at 5:37 PM, shashi shekhar <me_shashi29@yahoo.co.in> wrote:

Hi,

I want to add the the complete separate tool in galaxy . how will i do it ..i don't want to use existing visulaization tool.

Regards
shashi

From: Hans-Rudolf Hotz <hrh@fmi.ch>
To: shashi shekhar <me_shashi29@yahoo.co.in>
Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Sent: Wednesday, 19 June 2013 12:29 PM
Subject: Re: [galaxy-dev] visulaization tool

Hi Shashi

Have a look at:

http://wiki.galaxyproject.org/Learn/Visualization
http://wiki.galaxyproject.org/Visualization%20Setup


Regards, Hans-Rudolf



On 06/19/2013 08:07 AM, shashi shekhar wrote:
> Hi,
>
> i want to add new  visualization tool in galaxy . can i get the required
> documents ?
>
> can u send me the details how can i add the visualization tool in  galaxy .
>
>
>
> Regards
> shashi









___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/