Bug in cufflinks_wrapper.xml?
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 *******************************************************
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 *******************************************************
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participants (2)
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Curt Palm -
Jeremy Goecks