visualization button

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visualization button

philippe
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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Re: visualization button

Hans-Rudolf Hotz
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/
>
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Re: visualization button

philippe
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 <[hidden email]>:
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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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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   http://galaxyproject.org/search/mailinglists/



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Re: visualization button

Hans-Rudolf Hotz


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 <[hidden email]
> <mailto:[hidden email]>>:
>
>     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/>
>
>
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Re: visualization button

philippe
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 <[hidden email]>:


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 <[hidden email]
<mailto:[hidden email]>>:


    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/>




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in your mail client.  To manage your subscriptions to this
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Re: visualization button

Hans-Rudolf Hotz
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 <[hidden email]
> <mailto:[hidden email]>>:
>
>
>
>     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 <[hidden email]
>         <mailto:[hidden email]>
>         <mailto:[hidden email] <mailto:[hidden email]>>>:
>
>
>              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/>
>                  <http://galaxyproject.org/__search/mailinglists/
>         <http://galaxyproject.org/search/mailinglists/>>
>
>
>
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