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 */