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;
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