Hi, I have developed a simple script that give some statistics on an assemble. It generates a tabular output. The visualization button is not available when I extend the output in the history pane. Is there any code that I need to put in my xml wrapper to get this button available ? Regards, Philip
Hi Philip The appearance of the visualization button depends on the datatype of your output. E.g. when it is set to 'tabular', you should get the button allowing you to create a scatter plot. However, depending on your data, it might not make much sense to visualize it in 'Trackster', 'Circster' or as scatter plot. Regards, Hans-Rudolf On 04/07/2014 02:11 AM, Philippe Moncuquet wrote:
Hi,
I have developed a simple script that give some statistics on an assemble. It generates a tabular output. The visualization button is not available when I extend the output in the history pane. Is there any code that I need to put in my xml wrapper to get this button available ?
Regards, Philip
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Hi Rudolph, Thanks for the answer. I understand that it would make no sense to allow generation of graphics on non relevant data. My data is in tabular format and that is the reason why I was surprise not to see that button. <outputs> <data name="tabular_file" label="report.tsv" type="tabular" format="tabular" /> </outputs> I wouldn't be surprised if something was wrong in my syntax. Thanks for the help anyway. Cheers, Philip 2014-04-07 16:52 GMT+10:00 Hans-Rudolf Hotz <hrh@fmi.ch>:
Hi Philip
The appearance of the visualization button depends on the datatype of your output. E.g. when it is set to 'tabular', you should get the button allowing you to create a scatter plot.
However, depending on your data, it might not make much sense to visualize it in 'Trackster', 'Circster' or as scatter plot.
Regards, Hans-Rudolf
On 04/07/2014 02:11 AM, Philippe Moncuquet wrote:
Hi,
I have developed a simple script that give some statistics on an assemble. It generates a tabular output. The visualization button is not available when I extend the output in the history pane. Is there any code that I need to put in my xml wrapper to get this button available ?
Regards, Philip
___________________________________________________________ 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/
On 04/08/2014 02:05 AM, Philippe Moncuquet wrote:
Hi Rudolph,
Thanks for the answer. I understand that it would make no sense to allow generation of graphics on non relevant data. My data is in tabular format and that is the reason why I was surprise not to see that button.
<outputs> <data name="tabular_file" label="report.tsv" type="tabular" format="tabular" /> </outputs>
I would re-write this like: <outputs> <data name="tabular_file" label="report.tsv" format="tabular" /> </outputs> Also, make sure your output is actually a table, ie it does consist of more than one (tab-separated) column. Hans-Rudolf
I wouldn't be surprised if something was wrong in my syntax. Thanks for the help anyway.
Cheers, Philip
2014-04-07 16:52 GMT+10:00 Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>>:
Hi Philip
The appearance of the visualization button depends on the datatype of your output. E.g. when it is set to 'tabular', you should get the button allowing you to create a scatter plot.
However, depending on your data, it might not make much sense to visualize it in 'Trackster', 'Circster' or as scatter plot.
Regards, Hans-Rudolf
On 04/07/2014 02:11 AM, Philippe Moncuquet wrote:
Hi,
I have developed a simple script that give some statistics on an assemble. It generates a tabular output. The visualization button is not available when I extend the output in the history pane. Is there any code that I need to put in my xml wrapper to get this button available ?
Regards, Philip
_____________________________________________________________ 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/ <http://galaxyproject.org/search/mailinglists/>
Hi Hans-Rudolph, Ok so the syntax in the wrapper was not the problem. My file was tabular but the first column contained string and numbers whereas the second column contained only numbers. When I added a 3rd column with numbers to test I was able to see the button and generate some graphics. I wish It could have taken the first column as the label for the second but I understand that would produces unwanted behavior in other context. Anyway, all good, thanks for the help. Regards, Philip 2014-04-08 17:33 GMT+10:00 Hans-Rudolf Hotz <hrh@fmi.ch>:
On 04/08/2014 02:05 AM, Philippe Moncuquet wrote:
Hi Rudolph,
Thanks for the answer. I understand that it would make no sense to allow generation of graphics on non relevant data. My data is in tabular format and that is the reason why I was surprise not to see that button.
<outputs> <data name="tabular_file" label="report.tsv" type="tabular" format="tabular" /> </outputs>
I would re-write this like:
<outputs> <data name="tabular_file" label="report.tsv" format="tabular" /> </outputs>
Also, make sure your output is actually a table, ie it does consist of more than one (tab-separated) column.
Hans-Rudolf
I wouldn't be surprised if something was wrong in my syntax. Thanks for
the help anyway.
Cheers, Philip
2014-04-07 16:52 GMT+10:00 Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>>:
Hi Philip
The appearance of the visualization button depends on the datatype of your output. E.g. when it is set to 'tabular', you should get the button allowing you to create a scatter plot.
However, depending on your data, it might not make much sense to visualize it in 'Trackster', 'Circster' or as scatter plot.
Regards, Hans-Rudolf
On 04/07/2014 02:11 AM, Philippe Moncuquet wrote:
Hi,
I have developed a simple script that give some statistics on an assemble. It generates a tabular output. The visualization button is not available when I extend the output in the history pane. Is there any code that I need to put in my xml wrapper to get this button available ?
Regards, Philip
_____________________________________________________________
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/
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Philip Using a the first column as label should work if you tick the box "Include a third column as data point IDs?" Regards, Hans-Rudolf On 04/09/2014 07:47 AM, Philippe Moncuquet wrote:
Hi Hans-Rudolph,
Ok so the syntax in the wrapper was not the problem. My file was tabular but the first column contained string and numbers whereas the second column contained only numbers. When I added a 3rd column with numbers to test I was able to see the button and generate some graphics. I wish It could have taken the first column as the label for the second but I understand that would produces unwanted behavior in other context. Anyway, all good, thanks for the help.
Regards, Philip
2014-04-08 17:33 GMT+10:00 Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>>:
On 04/08/2014 02:05 AM, Philippe Moncuquet wrote:
Hi Rudolph,
Thanks for the answer. I understand that it would make no sense to allow generation of graphics on non relevant data. My data is in tabular format and that is the reason why I was surprise not to see that button.
<outputs> <data name="tabular_file" label="report.tsv" type="tabular" format="tabular" /> </outputs>
I would re-write this like:
<outputs> <data name="tabular_file" label="report.tsv" format="tabular" /> </outputs>
Also, make sure your output is actually a table, ie it does consist of more than one (tab-separated) column.
Hans-Rudolf
I wouldn't be surprised if something was wrong in my syntax. Thanks for the help anyway.
Cheers, Philip
2014-04-07 16:52 GMT+10:00 Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>>:
Hi Philip
The appearance of the visualization button depends on the datatype of your output. E.g. when it is set to 'tabular', you should get the button allowing you to create a scatter plot.
However, depending on your data, it might not make much sense to visualize it in 'Trackster', 'Circster' or as scatter plot.
Regards, Hans-Rudolf
On 04/07/2014 02:11 AM, Philippe Moncuquet wrote:
Hi,
I have developed a simple script that give some statistics on an assemble. It generates a tabular output. The visualization button is not available when I extend the output in the history pane. Is there any code that I need to put in my xml wrapper to get this button available ?
Regards, Philip
_________________________________________________________________
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To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/____search/mailinglists/ <http://galaxyproject.org/__search/mailinglists/> <http://galaxyproject.org/__search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>>
participants (2)
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Hans-Rudolf Hotz -
Philippe Moncuquet