Local display application questions
Hi Greg, I made a tool for Galaxy which produces a normal XML output file and next to that it also produces a HTML report with some quick summarized details for the user. I could solve this by using 2 output files, but I don't want to keep the history as concise as possible. To I found the option to use "display application". I defined my as below: <display id="sedmatreport" version="1.0.0" name="Show "> <link id="sedmatreport" name="SedMat_report"> <url target_frame="galaxy_main">${BASE_URL}/static/prims/reports/${dataset.id}/sedmat_report.html</url> </link> </display> So in my tool config xml I have the following respective configuration: <command interpreter=" java -jar "> Mytool.jar ...some parameters.... -outReport /galaxy-dist/static/prims/reports/$outputData.dataset.id/sedmat_report.html #end if </command> è This works fine, but I would like to avoid using the static directory. Do you know if there is an alternative web directory configured by default in the Galaxy web-server? è è I also want to avoid the /galaxy-dist/ part in the tool configuration since the Galaxy home directory can vary. Is there a variable which I can use for this? Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>
On Mon, Apr 2, 2012 at 2:00 PM, Lukasse, Pieter <pieter.lukasse@wur.nl> wrote:
Hi Greg,
I made a tool for Galaxy which produces a normal XML output file and next to that it also produces a HTML report with some quick summarized details for the user.
I could solve this by using 2 output files, but ...
That is the normal way to do this in Galaxy, isn't it? You can also use stdout for a small amount of plain text summary output - shown in the history as the 'info' text - perhaps that would be enough instead? Peter
As an alternative you can return "hidden" history items. Not exactly what you want perhaps... ________________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Peter Cock [p.j.a.cock@googlemail.com] Verzonden: maandag 2 april 2012 15:38 To: Lukasse, Pieter Cc: Greg Von Kuster (greg@bx.psu.edu); galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Local display application questions On Mon, Apr 2, 2012 at 2:00 PM, Lukasse, Pieter <pieter.lukasse@wur.nl> wrote:
Hi Greg,
I made a tool for Galaxy which produces a normal XML output file and next to that it also produces a HTML report with some quick summarized details for the user.
I could solve this by using 2 output files, but ...
That is the normal way to do this in Galaxy, isn't it? You can also use stdout for a small amount of plain text summary output - shown in the history as the 'info' text - perhaps that would be enough instead? Peter ___________________________________________________________ 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/
Hi Peter, Alex, Thanks for the tips, the stdout is very useful indeed for a small amount of information. However I want to display a large HTML report with some pictures/plots that will help the user assess the execution of the tool. A hidden output will also not work as I want the XML output item to be the visible one in the history. In the display application context I only get the datasetid of the history item that triggered it (afaik). Below a small impression of part of the report: [cid:image001.jpg@01CD18A0.F198CF50] Regards, Pieter. -----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: maandag 2 april 2012 15:38 To: Lukasse, Pieter Cc: Greg Von Kuster (greg@bx.psu.edu); galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Local display application questions On Mon, Apr 2, 2012 at 2:00 PM, Lukasse, Pieter <pieter.lukasse@wur.nl<mailto:pieter.lukasse@wur.nl>> wrote:
Hi Greg,
I made a tool for Galaxy which produces a normal XML output file and
next to that it also produces a HTML report with some quick summarized
details for the user.
I could solve this by using 2 output files, but ...
That is the normal way to do this in Galaxy, isn't it? You can also use stdout for a small amount of plain text summary output - shown in the history as the 'info' text - perhaps that would be enough instead? Peter
On Thu, Apr 12, 2012 at 10:39 AM, Lukasse, Pieter <pieter.lukasse@wur.nl> wrote:
Hi Peter, Alex,
Thanks for the tips, the stdout is very useful indeed for a small amount of information. However I want to display a large HTML report with some pictures/plots that will help the user assess the execution of the tool. A hidden output will also not work as I want the XML output item to be the visible one in the history. ...
Can you embed the HTML report into the XML file, so that displaying the XML file shows the report to the user (while retaining the nicely structured data for downstream analysis)? Alternatively, can you generate the HTML report from the XML file? If so, you could have a single XML output file, defined as an XML sub-class in Galaxy, with custom display handling which shows the user the HTML report instead of the raw XML. (I'm assuming that externally defined Galaxy datatypes can do that - if not perhaps that would be worth catering to.) Peter
participants (3)
-
Bossers, Alex -
Lukasse, Pieter -
Peter Cock