On Tue, Apr 10, 2018 at 3:28 PM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Hi Peter,
I can contact report the issue on github.
I think that would be best.
It looks like its looking for a variable called dataset with is not defined in the input part.
this looks like python code?:
##------------------------------------------------------------------------------------ ## This function returns the name of the sample associated to a given file ##------------------------------------------------------------------------------------ #def get_sample_name($dataset, $sample_mapping): ##If the file with samples mapping was provided #if $sample_mapping != None: #return $sample_mapping.get($dataset.name, None) ##Otherwise with extract the sample name from the filename #else: #return str($dataset.element_identifier) #end if #end def
Cheers Jochen
Sort of. It is a templating language called Cheetah which supports of lot of Python syntax: http://cheetahtemplate.org/ Most Galaxy wrappers at most use this for if-statements and for-loops, this might be the first time I've seen complicated functions being defined in Cheetah code like this. It would help greatly if the tool author provided a test dataset (and even better used this to define a tool self-test). Peter