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
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