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             cp...@stanford.edu
> Stanford Genome Technology Center
> 
> MC:  8307
> office: 650-812-1994        cell: 408 858-7849
> *******************************************************
> 
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