Curt,
You are correct, this is a bug. It was fixed in this changeset:
https://bitbucket.org/galaxy/galaxy-central/changeset/ff7c8c0bef60
We'll be updating galaxy-dist in the next week and this change will be
available then.
Thanks,
J.
On Oct 5, 2011, at 5:54 PM, Curt Palm wrote:
I have been having trouble getting cufflinks to run with the -g or -G
parameters via Galaxy. when I select either use reference annotation or
use reference annotation as guide from the pulldown menu, cufflinks runs ,
but the -g or -G is not added to the cufflinks command. I think I have
found the problem in the cufflinks_wrapper.xml file.
line17#if $reference_annotation.use_ref == use reference
annotation:
line18-G $reference_annotation.reference_annotation_file
line19#end if
line20#if $reference_annotation.use_ref == use reference
annotation guide:
line21-g
$reference_annotation_guide.reference_annotation_guide_file
.
line56 conditional name=reference_annotation
line57param name=use_ref type=select label=Use Reference
Annotation
line58option value=NoNo/option
line59option value=Use reference annotationUse reference
annotation/option
line60option value=Use reference annotation guideUse
reference annotation as guide/option
line61/param
note that Use is capitalized in lines57 and 59 but not in lines 17 and 20.
I made these changes in lines 17,20 and 21 and I now get the -G and -g
are passed to the cuffflinks command
use to Use in lines 17 and 20
reference_annotation_guide.reference_annotation_guide_file to
reference_annotation.reference_annotation_guide_file in line 21
line17#if $reference_annotation.use_ref == Use reference
annotation:
line18-G $reference_annotation.reference_annotation_file
line19#end if
line20#if $reference_annotation.use_ref == Use reference
annotation guide:
line21-g $reference_annotation.reference_annotation_guide_file
-curt
***
Curtis J. Palm cp...@stanford.edu
Stanford Genome Technology Center
MC: 8307
office: 650-812-1994cell: 408 858-7849
***
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