external display application styles

17 Sep 2010

      Hi all,
I need the users to see the direct link for BAM files so that they can copy/paste it in their desktop visualizer (either IGV, IGB, whatever...).
I could write the application xml definition and it works properly:

<display id="igv_bam" version="1.0.0" name="view link for">
    <link id="igv" name="IGV">
        <url>$track.url</url>
        <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" />
        <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /><!-- UCSC expects index file to exist as bam_file_name.bai -->
        <param type="template" name="track" viewable="True" strip_https="True">
Select "File -> Load from URL..." in IGV, then copy the following link:

${bam_file.url}
</param>
    </link>
</display>

I just would like now to have this page using galaxy css so that I can write nicer instruction (with colors and images) for the dummiest end-user. I see that the resulting page source encloses everything between <pre/> tags:

<html>
  <body>
    <pre style="word-wrap: break-word; white-space: pre-wrap;">
      "
        HERE IS THE CONTENT OF THE APPLICATION
      "
    </pre>
  </body>
</html>

How can I override this behavior? I mean, I can edit the template (which is the template?) but that would affect every other display application...

Thanks

d
/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: davide.cittaro@ifom-ieo-campus.it
*/

Davide Cittaro

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