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"> line57 <param name="use_ref" type="select" label="Use Reference Annotation"> line58 <option value="No">No</option> line59 <option value="Use reference annotation">Use reference annotation</option> line60 <option value="Use reference annotation guide">Use 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 cpalm@stanford.edu Stanford Genome Technology Center
MC: 8307 office: 650-812-1994 cell: 408 858-7849 *******************************************************
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: