Thon, I just had an idea - write a new tool that takes an Html dataset from
the user's history and a file specification (eg "foo.xls") and 'promotes'
the file(s) in the extra_files_path that match the file specification into
new history items?
That way you can automate the process - of course, including the outputs in
workflows when their number is not known at execution may be tricky, but at
least this is a generic approach and won't require any changes to any of
the tools that generate Html outputs?


On Tue, Feb 21, 2012 at 8:45 AM, Anthonius deBoer <thondeb...@me.com> wrote:

> Hi Ross,
>
> Thanks for the reply...It is indeed as I feared...I'll probably refactor
> the code so the user is able to get the actual output files.
>
> Thon
>
> On Feb 20, 2012, at 01:29 PM, Ross <ross.laza...@gmail.com> wrote:
>
> Hi, Thon,
>
> On Tue, Feb 21, 2012 at 6:47 AM, Thon Deboer <thondeb...@me.com> wrote:
>
>> Hi,
>>
>> Is there a way to extract the individual files from a composite file,
>> such as the HTML files created by the picard tools?
>>
>
> The decision to hide multiple outputs in a single history html object has
> this as a downside to the benefits of less cluttered histories.
> The results you want can be manually extracted in the usual ways - eg
> pasting the relevant html page url into an upload box.. but that doesn't
> solve your challenge of automating the process for a very large number of
> datasets.
>
> One possible solution is to add some complexity to each of the relevant
> tool forms to allow the user to specifically nominate outputs to be
> returned as individual new history datasets.
> It is not a huge task but it's not as far as I'm aware, high on the list
> of priorities for the team.
>
> If you are motivated sufficiently to fix this so it can do what you need,
> contributions of code to improve Galaxy tools are always very welcome ?
>
>
>> I would like to take the metrics files and use them further down in some
>> workflow, but I only get an HTML file...
>> While these HTML files are nice for quickly looking at the results of one
>> or two files, it becomes a problem if you have 88 samples like I do...
>>
>> I hate to have to re-write all the picard tools to produce actual files,
>> but maybe there is something I am missing about composite datatype files?
>> The wiki only explains how to CREATE them, not how to use those files
>> downstream....
>>
>> Regards,
>>
>> Thon de Boer, Ph.D.
>> Bioinformatics Guru
>> +1-650-799-6839
>>
>> thondeb...@me.com
>>
>> LinkedIn Profile <http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b>
>>
>>
>>
>>
>>
>>
>> ___________________________________________________________
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>
>
>
> --
> Ross Lazarus MBBS MPH;
> Associate Professor, Harvard Medical School;
> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
>
>


-- 
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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