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...).
<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
*/