qiime longitudinal maturity-index

--i-table=$itable
--p-state-column="$pstatecolumn"
--p-group-by="$pgroupby"
--p-control="$pcontrol"

#if str($pindividualidcolumn):
 --p-individual-id-column="$pindividualidcolumn"
#end if

#if str($pestimator) != 'None':
 --p-estimator=$pestimator
#end if

#if str($pnestimators):
 --p-n-estimators=$pnestimators
#end if

#if str($ptestsize):
 --p-test-size=$ptestsize
#end if

#if str($pstep):
 --p-step=$pstep
#end if

#if str($pcv):
 --p-cv=$pcv
#end if

#if str($prandomstate):
 --p-random-state="$prandomstate"
#end if

#set $pnjobs = '${GALAXY_SLOTS:-4}'
#if str($pnjobs):
 --p-n-jobs="$pnjobs"
#end if


#if $pparametertuning:
 --p-parameter-tuning
#end if

#if $poptimizefeatureselection:
 --p-optimize-feature-selection
#end if

#if $pstratify:
 --p-stratify
#end if

#if str($pmissingsamples) != 'None':
 --p-missing-samples=$pmissingsamples
#end if

#if str($pfeaturecount):
 --p-feature-count=$pfeaturecount
#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-sample-estimator=osampleestimator
--o-feature-importance=ofeatureimportance
--o-predictions=opredictions
--o-model-summary=omodelsummary
--o-accuracy-results=oaccuracyresults
--o-maz-scores=omazscores
--o-clustermap=oclustermap
--o-volatility-plots=ovolatilityplots
;
cp osampleestimator.qza $osampleestimator;
cp ofeatureimportance.qza $ofeatureimportance;
cp opredictions.qza $opredictions;
qiime tools export --input-path omodelsummary.qzv --output-path out   && mkdir -p '$omodelsummary.files_path'
&& cp -r out/* '$omodelsummary.files_path'
&& mv '$omodelsummary.files_path/index.html' '$omodelsummary';
qiime tools export --input-path oaccuracyresults.qzv --output-path out   && mkdir -p '$oaccuracyresults.files_path'
&& cp -r out/* '$oaccuracyresults.files_path'
&& mv '$oaccuracyresults.files_path/index.html' '$oaccuracyresults';
cp omazscores.qza $omazscores;
qiime tools export --input-path oclustermap.qzv --output-path out   && mkdir -p '$oclustermap.files_path'
&& cp -r out/* '$oclustermap.files_path'
&& mv '$oclustermap.files_path/index.html' '$oclustermap';
qiime tools export --input-path ovolatilityplots.qzv --output-path out   && mkdir -p '$ovolatilityplots.files_path'
&& cp -r out/* '$ovolatilityplots.files_path'
&& mv '$ovolatilityplots.files_path/index.html' '$ovolatilityplots'