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             cp...@stanford.edu
Stanford Genome Technology Center

MC:  8307
office: 650-812-1994        cell: 408 858-7849
*******************************************************

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