qiime longitudinal pairwise-differences

--p-metric="$pmetric"
--p-state-column="$pstatecolumn"
--p-state-1="$pstate1"
--p-state-2="$pstate2"


#if '__sq__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if str($pindividualidcolumn):
 --p-individual-id-column="$pindividualidcolumn"
#end if



#if str($itable) != 'None':
 --i-table=$itable
#end if

#if str($pgroupcolumn):
 --p-group-column="$pgroupcolumn"
#end if

#if $pparametric:
 --p-parametric
#end if

#if str($ppalette) != 'None':
 --p-palette=$ppalette
#end if

#if str($preplicatehandling) != 'None':
 --p-replicate-handling=$preplicatehandling
#end if


#if $input_files_mmetadatafile:
#def list_dict_to_string(list_dict):
	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
	#for d in list_dict[1:]:
		#set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
	#end for
	#return $file_list
#end def
 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
#end if


--o-visualization=ovisualization
;
qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
&& cp -r out/* '$ovisualization.files_path'
&& mv '$ovisualization.files_path/index.html' '$ovisualization';